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OnderzoekMolecular Dynamics GroupPublications

Publications

2017

Bartelds, R., Barnoud, J., J. Boersma, A., J. Marrink, S., & Poolman, B. (2017). Lipid phase separation in the presence of hydrocarbons in giant unilamellar vesicles. AIMS Biophysics, 4(4), 528-542. DOI: 10.3934/biophy.2017.4.528
Hsu, P-C., Bruininks, B. M. H., Jefferies, D., Cesar Telles de Souza, P., Lee, J., Patel, D. S., ... Im, W. (2017). CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. Journal of Computational Chemistry, 38, 2354-2363. DOI: 10.1002/jcc.24895
Uusitalo, J. J., Ingolfsson, H. I., Marrink, S. J., & Faustino, I. (2017). Martini Coarse-Grained Force Field: Extension to RNA. Biophysical Journal, 113(2), 246-256. DOI: 10.1016/j.bpj.2017.05.043
Frederix, P. W. J. M., Idé, J., Altay, Y., Schaeffer, G., Surin, M., Beljonne, D., ... Marrink, S. J. (2017). Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles. Acs Nano. DOI: 10.1021/acsnano.7b02211
Faustino, I., & Marrink, S. J. (2017). cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations. Bioinformatics, [btx444]. DOI: 10.1093/bioinformatics/btx444
Van Eerden, F. J., Melo, M. N., Frederix, P. W. J. M., Periole, X., & Marrink, S. J. (2017). Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nature Communications, 8, 1-8. [ncomms15214]. DOI: 10.1038/ncomms15214
Liu, B., Åberg, C., van Eerden, F. J., Marrink, S., Poolman, B., & Boersma, A. J. (2017). Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding. Biophysical Journal, 112(9), 1929-1939. DOI: 10.1016/j.bpj.2017.04.004
Gu, R-X., Ingólfsson, H. I., De Vries, A. H., Marrink, S. J., & Tieleman, D. P. (2017). Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations. Journal of Physical Chemistry B, 121(15), 3262–3275. [jpcb.6b07142]. DOI: 10.1021/acs.jpcb.6b07142
van Eerden, F. J., van den Berg, T., Frederix, P. W. J. M., de Jong, D. H., Periole, X., & Marrink, S. J. (2017). Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane. Journal of Physical Chemistry B., 121(15), 3237–3249. [jpcb.6b06865]. DOI: 10.1021/acs.jpcb.6b06865
Venable, R. M., Ingólfsson, H. I., Lerner, M. G., Perrin, B. S., Camley, B. A., Marrink, S. J., ... Pastor, R. W. (2017). Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions. The Journal of Physical Chemistry B, 121(15), 3443–3457. [jpcb.6b09111]. DOI: 10.1021/acs.jpcb.6b09111
Melo, M. N., Arnarez, C., Sikkema, H., Kumar, N., Walko, M., Berendsen, H. J. C., ... Ingólfsson, H. I. (2017). High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. Journal of the American Chemical Society, 139(7), 2664-2671. DOI: 10.1021/jacs.6b11091
Alessandri, R., Uusitalo, J. J., De Vries, A. H., Havenith, R. W. A., & Marrink, S. J. (2017). Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations. Journal of the American Chemical Society, 139 (10), 3697–3705. [jacs.6b11717]. DOI: 10.1021/jacs.6b11717
Maingi, V., Burns, J. R., Uusitalo, J. J., Howorka, S., Marrink, S. J., & Sansom, M. S. P. (2017). Stability and dynamics of membrane-spanning DNA nanopores. Nature Communications, 8, 1-12. [14784]. DOI: 10.1038/ncomms14784
Arnarez, C., & Marrink, S. J. (2017). Chapter 1: Computational Microscopy of Mitochondrial Membranes. In K. Kholmurodov (Ed.), Computer Design for New Drugs and Materials: Molecular Dynamics of Nanoscale Phenomena (pp. 1). Nova Science Publishers.
Swier, L. J. Y. M., Monjas, L., Reeßing, F., Oudshoorn, R. C., Aisyah, A., Primke, T., ... Slotboom, D. J. (2017). Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations. MedChemCommun, 8(5), 1121-1130. DOI: 10.1039/C7MD00079K
Kanduc, M., Schlaich, A., de Vries, A. H., Jouhet, J., Marechal, E., Deme, B., ... Schneck, E. (2017). Tight cohesion between glycolipid membranes results from balanced water-headgroup interactions. Nature Communications, 8, [14899]. DOI: 10.1038/ncomms14899

2016

Zavadlav, J., Podgornik, R., Melo, M., Marrink, S., & Praprotnik, M. (2016). Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution. European physical journal-Special topics, 225(8-9), 1595-1607. DOI: 10.1140/epjst/e2016-60117-8
Zavadlav, J., Marrink, S. J., & Praprotnik, M. (2016). Adaptive resolution simulation of supramolecular water: The concurrent making, breaking, and remaking of water bundles. Journal of Chemical Theory and Computation, 12(8), 4138-4145. [6b00536]. DOI: 10.1021/acs.jctc.6b00536
Smeets, C. J. L. M., Zmorzynska, J., Melo, M. N., Stargardt, A., Dooley, C., Bakalkin, G., ... Verbeek, D. S. (2016). Altered secondary structure of Dynorphin A associates with loss of opioid signalling and NMDA-mediated excitotoxicity in SCA23. Human Molecular Genetics, 25(13), 2728-2737. DOI: 10.1093/hmg/ddw130
Arnarez, C., Marrink, S. J., & Periole, X. (2016). Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes. Chemical Science, 7, 4435-4443. [10.1039/C5SC04664E]. DOI: 10.1039/C5SC04664E
De Jong, D. H., Baoukina, S., Ingólfsson, H., & Marrink, S. J. (2016). Martini straight: Boosting performance using a shorter cutoff and GPUs. Computer Physics Communications, 199, 1-7. DOI: 10.1016/j.cpc.2015.09.014
Ingólfsson, H. I., Arnarez, C., Periole, X., & Marrink, S. J. (2016). Computational 'microscopy' of cellular membranes. Journal of Cell Science, 129(2), 257-268. DOI: 10.1242/jcs.176040
Antillón, A., De Vries, A. H., Espinosa-caballero, M., Falcón-gonzález, J. M., Flores Romero, D., González–damián, J., ... Johnson, C. J. (Ed.) (2016). An Amphotericin B Derivative Equally Potent to Amphotericin B and with Increased Safety. PLoS ONE, 11(9), 1-38. [e0162171]. DOI: 10.1371/journal.pone.0162171
Guskov, A., Jensen, S., Faustino, I., Marrink, S. J., & Slotboom, D. J. (2016). Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk. Nature Communications, 7, 1-6. [ncomms13420]. DOI: 10.1038/ncomms13420
Paulechka, E., Wassenaar, T., Kroenlein, K., Kazakov, A., & Smolyanitsky, A. (2016). Nucleobase-functionalized grapheme nanoribbons for accurate high-speed DNA sequencing. Nanoscale, 8, 1861-1867. DOI: 10.1039/C5NR07061A

2015

Melo, M. N., Ingolfsson, H. I., & Marrink, S. J. (2015). Parameters for Martini sterols and hopanoids based on a virtual-site description. The Journal of Chemical Physics, 143(24), 1-12. [243152]. DOI: 10.1063/1.4937783
Uytterhoeven, V., Lauwers, E., Maes, I., Miskiewicz, K., Melo, M., Swerts, J., ... Verstreken, P. (2015). Hsc70-4 Deforms Membranes to Promote Synaptic Protein Turnover by Endosomal Microautophagy. Neuron, 88(4), 735-748. DOI: 10.1016/j.neuron.2015.10.012
Liguori, N., Periole, X., Marrink, S. J., & Croce, R. (2015). From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII). Scientific Reports, 5, [15661]. DOI: 10.1038/srep15661
Qi, Y., Ingolfsson, H. I., Cheng, X., Lee, J., Marrink, S. J., & Im, W. (2015). CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field. Journal of Chemical Theory and Computation, 11(9), 4486-4494. DOI: 10.1021/acs.jctc.5b00513
Uusitalo, J. J., Ingolfsson, H. I., Akhshi, P., Tieleman, D. P., & Marrink, S. J. (2015). Martini Coarse-Grained Force Field: Extension to DNA. Journal of Chemical Theory and Computation, 11(8), 3932-3945. DOI: 10.1021/acs.jctc.5b00286
Zavadlav, J., Melo, M. N., Marrink, S. J., & Praprotnik, M. (2015). Adaptive resolution simulation of polarizable supramolecular coarse-grained water models. Journal of Chemical Physics, 142(24), [244118]. DOI: 10.1063/1.4923008
de Jong, D. H., Liguori, N., van den Berg, T., Arnarez, C., Periole, X., & Marrink, S. J. (2015). Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex. The Journal of Physical Chemistry B, 119(25), 7791-7803. DOI: 10.1021/acs.jpcb.5b00809
van Eerden, F. J., de Jong, D. H., de Vries, A. H., Wassenaar, T. A., & Marrink, S. J. (2015). Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations. Biochimica et Biophysica Acta-Biomembranes, 1848(6), 1319-1330. DOI: 10.1016/j.bbamem.2015.02.025
Wassenaar, T. A., Pluhackova, K., Moussatova, A., Sengupta, D., Marrink, S. J., Tieleman, D. P., & Boeckrnann, R. A. (2015). High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. Journal of Chemical Theory and Computation, 11(5), 2278-2291. DOI: 10.1021/ct5010092
Wassenaar, T. A., Ingolfsson, H. I., Boeckmann, R. A., Tieleman, D. P., & Marrink, S. J. (2015). Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations. Journal of Chemical Theory and Computation, 11(5), 2144-2155. DOI: 10.1021/acs.jctc.5b00209
Goga, N., Melo, M. N., Rzepiela, A. J., de Vries, A., Hadar, A., Marrink, S. J., & Berendsen, H. (2015). Benchmark of Schemes for Multiscale Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 11(4), 1389-1398. DOI: 10.1021/ct501102b
Heberling, M. M., Masman, M. F., Bartsch, S., Wybenga, G. G., Dijkstra, B. W., Marrink, S. J., & Janssen, D. B. (2015). Ironing out Their Differences: Dissecting the Structural Determinants of a Phenylalanine Aminomutase and Ammonia Lyase. ACS chemical biology, 10(4), 989-997. DOI: 10.1021/cb500794h
Wijma, H. J., Floor, R. J., Bjelic, S., Marrink, S. J., Baker, D., & Janssen, D. B. (2015). Enantioselective Enzymes by Computational Design and In Silico Screening. Angewandte Chemie - International Edition, 54(12), 3726-3730. DOI: 10.1002/anie.201411415
Lopez, C. A., Bellesia, G., Redondo, A., Langan, P., Chundawat, S. P. S., Dale, B. E., ... Gnanakaran, S. (2015). MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers. The Journal of Physical Chemistry B, 119(2), 465-473. DOI: 10.1021/jp5105938
Arnarez, C., Uusitalo, J. J., Masman, M. F., Ingolfsson, H. I., de Jong, D. H., Melo, M. N., ... Marrink, S. J. (2015). Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simblations with Implicit Solvent. Journal of Chemical Theory and Computation, 11(1), 260-275. DOI: 10.1021/ct500477k
van der Velde, J. H. M., Uusitalo, J. J., Ugen, L-J., Warszawik, E. M., Herrmann, A., Marrink, S. J., & Cordes, T. (2015). Intramolecular photostabilization via triplet-state quenching: design principles to make organic fluorophores "self-healing". Faraday Discussions. DOI: 10.1039/c5fd00114e

2014

Konijnenberg, A., Yilmaz, D., Ingólfsson, H. I., Dimitrova, A., Marrink, S. J., Li, Z., ... Koçer, . A. (2014). Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America, 111(48), 17170-17175. DOI: 10.1073/pnas.1413118111
Ingólfsson, H. I., Melo, M. N., van Eerden, F. J., Arnarez, C., Lopez, C. A., Wassenaar, T. A., ... Marrink, S. J. (2014). Lipid organization of the plasma membrane. Journal of the American Chemical Society, 136(41), 14554-9. DOI: 10.1021/ja507832e
Moiset, G., López, C. A., Bartelds, R., Syga, L., Rijpkema, E., Cukkemane, A., ... Marrink, S. J. (2014). Disaccharides Impact the Lateral Organization of Lipid Membranes. Journal of the American Chemical Society. DOI: 10.1021/ja505476c
Barnoud, J., Rossi, G., Marrink, S. J., & Monticelli, L. (2014). Hydrophobic compounds reshape membrane domains. PLoS Computational Biology, 10(10), e1003873. DOI: 10.1371/journal.pcbi.1003873
Mukherjee, N., Jose, M., Birkner, J. P., Walko, M., Ingolfsson, H. I., Dimitrova, A., ... Kocer, A. (2014). The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension-induced gating. The FASEB Journal, 28(10), 4292-4302. DOI: 10.1096/fj.14-251579
Ingólfsson, H. I., Thakur, P., Herold, K. F., Hobart, E. A., Ramsey, N. B., Periole, X., ... Andersen, O. S. (2014). Phytochemicals Perturb Membranes and Promiscuously Alter Protein Function. ACS chemical biology, 9(8), 1788-1798. DOI: 10.1021/cb500086e
Milicevic, Z., Marrink, S. J., Smith, A-S., & Smith, D. M. (2014). Establishing conditions for simulating hydrophobic solutes in electric fields by molecular dynamics Effects of the long-range van der Waals treatment on the apparent particle mobility. Journal of Molecular Modeling, 20(8), [2359]. DOI: 10.1007/s00894-014-2359-5
Floor, R. J., Wijma, H. J., Colpa, D. I., Ramos-Silva, A., Jekel, P. A., Szymanski, W., ... Janssen, D. B. (2014). Computational Library Design for Increasing Haloalkane Dehalogenase Stability. ChemBioChem, 15(11), 1659-1671. DOI: 10.1002/cbic.201402128
Wijma, H. J., Marrink, S. J., & Janssen, D. B. (2014). Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations. Journal of chemical information and modeling, 54(7), 2079-2092. DOI: 10.1021/ci500126x
Zavadlav, J., Melo, M. N., Cunha, A. V., de Vries, A. H., Marrink, S. J., & Praprotnik, M. (2014). Adaptive Resolution Simulation of MARTINI Solvents. Journal of Chemical Theory and Computation, 10(6), 2591-2598. DOI: 10.1021/ct5001523
Campelo, F., Arnarez, C., Marrink, S. J., & Kozlov, M. M. (2014). Helfrich model of membrane bending: from Gibbs theory of liquid interfaces to membranes as thick anisotropic elastic layers. Progress in Colloid and Interface Science, 208, 25-33. DOI: 10.1016/j.cis.2014.01.018
Ingolfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., & Marrink, S. J. (2014). The power of coarse graining in biomolecular simulations. Wiley Interdisciplinary Reviews. Computational Molecular Science, 4(3), 225-248. DOI: 10.1002/wcms.1169
Kozlov, M. M., Campelo, F., Liska, N., Chernomordik, L. V., Marrink, S. J., & McMahon, H. T. (2014). Mechanisms shaping cell membranes. Current Opinion in Cell Biology, 29C, 53-60. DOI: 10.1016/j.ceb.2014.03.006
Pannuzzo, M., De Jong, D. H., Raudino, A., & Marrink, S. J. (2014). Simulation of polyethylene glycol and calcium-mediated membrane fusion. Journal of Chemical Physics, 140(12), [124905]. DOI: 10.1063/1.4869176
Zavadlav, J., Melo, M. N., Marrink, S. J., & Praprotnik, M. (2014). Adaptive resolution simulation of an atomistic protein in MARTINI water. The Journal of Chemical Physics, 140(5), [054114]. DOI: 10.1063/1.4863329
Wijma, H. J., Floor, R. J., Jekel, P. A., Baker, D., Marrink, S. J., & Janssen, D. B. (2014). Computationally designed libraries for rapid enzyme stabilization. Protein Engineering, Design & Selection, 27(2), 49-58. DOI: 10.1093/protein/gzt061
Wassenaar, T. A., Pluhackova, K., Böckmann, R. A., Marrink, S. J., & Tieleman, D. P. (2014). Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. Journal of Chemical Theory and Computation, 10(2), 676-690. DOI: 10.1021/ct400617g
Peters, E. A. J. F., Goga, N., & Berendsen, H. (2014). Stochastic Dynamics with Correct Sampling for Constrained Systems. Journal of Chemical Theory and Computation, 10(10), 4208-4220. DOI: 10.1021/ct500380x
Haverkort, F., Stradomska, A., Vries, A. H. D., & Knoester, J. (2014). First-Principles Calculation of the Optical Properties of an Amphiphilic Cyanine Dye Aggregate. The Journal of Physical Chemistry. A: Molecules, Spectroscopy, Kinetics, Environment, & General Theory, 118(6), 1012-1023. DOI: 10.1021/jp4112487
Negro, E., Latsuzbaia, R., de Vries, A. H., & Koper, G. J. M. (2014). Experimental and molecular dynamics characterization of dense micro emulsion systems morphology, conductivity and SAXS. Soft Matter, 10(43), 8685-8697. DOI: 10.1039/c4sm01763c
Boscia, A. L., Treece, B. W., Mohammadyani, D., Klein-Seetharaman, J., Braun, A. R., Wassenaar, T., ... Tristram-Nagle, S. (2014). X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes. Chemistry and Physics of Lipids, 178, 1-10. DOI: 10.1016/j.chemphyslip.2013.12.010

2013

Baaden, M., & Marrink, S. J. (2013). Coarse-grain modelling of protein-protein interactions. Current Opinion in Structural Biology, 23(6), 878-886. DOI: 10.1016/j.sbi.2013.09.004
Gobbo, C., Beurroies, I., de Ridder, D., Eelkema, R., Marrink, S. J., De Feyter, S., ... de Vries, A. H. (2013). MARTINI Model for Physisorption of Organic Molecules on Graphite. Journal of Physical Chemistry C, 117(30), 15623-15631. DOI: 10.1021/jp402615p
Bulacu, M., Goga, N., Zhao, W., Rossi, G., Monticelli, L., Periole, X., ... Marrink, S. J. (2013). Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 9(8), 3282-3292. DOI: 10.1021/ct400219n
Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2013). Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Scientific Reports, 3, 2071-1-2071-6. [2071]. DOI: 10.1038/srep02071
Raudino, A., Marrink, S. J., & Pannuzzo, M. (2013). Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: A theoretical and computational study. Journal of Chemical Physics, 138(23), 234901-1-234901-16. [234901]. DOI: 10.1063/1.4809993
van Hell, A. J., Melo, M. N., van Blitterswijk, W. J., Gueth, D. M., Braumuller, T. M., Pedrosa, L. R. C., ... Verheij, M. (2013). Defined lipid analogues induce transient channels to facilitate drug-membrane traversal and circumvent cancer therapy resistance. Scientific Reports, 3, 1-8. [1949]. DOI: 10.1038/srep01949
Gomulya, W., Costanzo, G. D., Figueiredo de Carvalho, E., Bisri, S. Z., Derenskyi, V., Fritsch, M., ... Loi, M. A. (2013). Semiconducting single-walled carbon nanotubes on demand by polymer wrapping. Advanced Materials, 25(21), 2948-2956. DOI: 10.1002/adma.201300267
Moiset, G., Cirac, A. D., Stuart, M. C. A., Marrink, S-J., Sengupta, D., & Poolman, B. (2013). Dual action of BPC194: a membrane active peptide killing bacterial cells. PLoS ONE, 8(4), [61541]. DOI: 10.1371/journal.pone.0061541
Wassenaar, T. A., Ingólfsson, H. I., Priess, M., Marrink, S. J., & Schaefer, L. V. (2013). Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained Biomolecular Simulations. Journal of Physical Chemistry B, 117(13), 3516-3530. DOI: 10.1021/jp311533p
Lopez, C. A., Sovova, Z., van Eerden, F. J., de Vries, A. H., & Marrink, S. J. (2013). Martini Force Field Parameters for Glycolipids. Journal of Chemical Theory and Computation, 9(3), 1694-1708. DOI: 10.1021/ct3009655
Arnarez, C., Mazat, J-P., Elezgaray, J., Marrink, S-J., & Periole, X. (2013). Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc(1). Journal of the American Chemical Society, 135(8), 3112-3120. DOI: 10.1021/ja310577u
Arnarez, C., Marrink, S. J., & Periole, X. (2013). Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Scientific Reports, 3(21), 1263-1-1263-8. [1263]. DOI: 10.1038/srep01263
Liang, C., Louhivuori, M., Marrink, S. J., Jansen, T. L. C., & Knoester, J. (2013). Vibrational Spectra of a Mechanosensitive Channel. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4(3), 448-452. DOI: 10.1021/jz3019258
de Jong, D. H., Singh, G., Bennett, W. F. D., Arnarez, C., Wassenaar, T. A., Schafer, L. V., ... Marrink, S. J. (2013). Improved Parameters for the Martini Coarse-Grained Protein Force Field. Journal of Chemical Theory and Computation, 9(1), 687-697. DOI: 10.1021/ct300646g
de Jong, D. H., Lopez, C. A., & Marrink, S. J. (2013). Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Faraday Discussions, 161, 347-363. DOI: 10.1039/c2fd20086d
Hu, M., de Jong, D. H., Marrink, S. J., & Deserno, M. (2013). Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model. Faraday Discussions, 161, 365-382. DOI: 10.1039/c2fd20087b
Marrink, S. J., & Tieleman, D. P. (2013). Perspective on the Martini model. Chemical Society Reviews, 42(16), 6801-6822. DOI: 10.1039/c3cs60093a
Smirnova, Y. G., Aeffner, S., Risselada, H. J., Salditt, T., Marrink, S. J., Mueller, M., & Knecht, V. (2013). Interbilayer repulsion forces between tension-free lipid bilayers from simulation. Soft Matter, 9(45), 10705-10718. DOI: 10.1039/c3sm51771c
Periole, X., & Marrink, S. J. (2013). The Martini Coarse-Grained Force Field. In L. Monticelli, & E. Salonen (Eds.), Biomolecular Simulations: Methods and Protocols (1 ed., Vol. 1, pp. 533-565). (Methods in Molecular Biology; Vol. 924). Springer International Publishing. DOI: 10.1007/978-1-62703-017-5
Haverkort, F., Stradomska, A., de Vries, A. H., & Knoester, J. (2013). Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations. Journal of Physical Chemistry B, 117(19), 5857-5867. DOI: 10.1021/jp4005696
Carrillo-Tripp, M., Periole, X., Garcia-Gonzalez, A., Espinosa-Caballero, M., Vargas-Gonzalez, C., de Vries, A. H., & Ortega-Blake, I. (2013). Aggregation States Driven by Dipole Interactions Regulates Action Mechanism of Polyene Antibiotics. Biophysical Journal, 104(2), 666A.

2012

Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2012). Amylose folding under the influence of lipids. Carbohydrate Research, 364, 1-7. DOI: 10.1016/j.carres.2012.10.007
Goga, N., Rzepiela, A. J., de Vries, A. H., Marrink, S. J., & Berendsen, H. J. C. (2012). Efficient Algorithms for Langevin and DPD Dynamics. Journal of Chemical Theory and Computation, 8(10), 3637-3649. DOI: 10.1021/ct3000876
Vandersteen, A., Masman, M. F., Baets, G. D., Jonckheere, W., Werf, K. V. D., Marrink, S. J., ... Broersen, K. (2012). Molecular plasticity regulates oligomerization and cytotoxicity of the multipeptide-length amyloid-β peptide pool. The Journal of Biological Chemistry, 287(44), 36732-36743. DOI: 10.1074/jbc.M112.394635
Deplazes, E., Louhivuori, M., Jayatilaka, D., Marrink, S. J., & Corry, B. (2012). Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations. PLoS Computational Biology, 8(9), e1002683-1-e1002683-1. [1002683]. DOI: 10.1371/journal.pcbi.1002683
Periole, X., Knepp, A. M., Sakmar, T. P., Marrink, S. J., & Huber, T. (2012). Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers. Journal of the American Chemical Society, 134(26), 10959-10965. DOI: 10.1021/ja303286e
Risselada, H. J., Marelli, G., Fuhrmans, M., Smirnova, Y. G., Grubmueller, H., Marrink, S. J., & Mueller, M. (2012). Line-Tension Controlled Mechanism for Influenza Fusion. Plos one, 7(6), [38302]. DOI: 10.1371/journal.pone.0038302
Baoukina, S., Marrink, S. J., & Tieleman, D. P. (2012). Molecular Structure of Membrane Tethers. Biophysical Journal, 102(8), 1866-1871. DOI: 10.1016/j.bpj.2012.03.048
Domanski, J., Marrink, S. J., & Schäfer, L. V. (2012). Transmembrane helices can induce domain formation in crowded model membranes. Biochimica et Biophysica Acta-Biomembranes, 1818(4), 984-994. DOI: 10.1016/j.bbamem.2011.08.021
Knepp, A. M., Periole, X., Marrink, S-J., Sakmar, T. P., & Huber, T. (2012). Rhodopsin Forms a Dimer with Cytoplasmic Helix 8 Contacts in Native Membranes. Biochemistry, 51(9), 1819-1821. DOI: 10.1021/bi3001598
de Jong, D. H., Periole, X., & Marrink, S. J. (2012). Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields. Journal of Chemical Theory and Computation, 8(3), 1003-1014. DOI: 10.1021/ct200599d
Huber, T., Periole, X., Knepp, A. M., Marrink, S-J., Mukhopadhyay, P., & Sakmar, T. P. (2012). Dynamic Assembly of the Receptor-G-Protein Signaling Complex. Biophysical Journal, 102(3), 516a-516a. [2930]. DOI: 10.1016/j.bpj.2011.11.2823
Periole, X., Knepp, A. M., Sakmar, T. P., Marrink, S-J., & Huber, T. (2012). Probing the Receptor Dimer Interfaces of G-Protein Coupled Receptor in Model Membranes. Biophysical Journal, 102(3), 515a-516a. DOI: 10.1016/j.bpj.2011.11.2822
Wassenaar, T. A., Schafer, L. V., Ingolfsson, H., & Marrink, S-J. (2012). Mixing Martinis: Atomistic Simulations of MscL in a Coarse Grained Environment. Biophysical Journal, 102(3), 241a-241a. DOI: 10.1016/j.bpj.2011.11.1326
Fuhrmans, M., & Marrink, S. J. (2012). Molecular View of the Role of Fusion Peptides in Promoting Positive Membrane Curvature. Journal of the American Chemical Society, 134(3), 1543-1552. DOI: 10.1021/ja207290b
Bulacu, M., Periole, X., Marrink, S. J., & Périole, X. (2012). In Silico Design of Robust Bolalipid Membranes. Biomacromolecules, 13(1), 196-205. DOI: 10.1021/bm201454J
Goga, N., Marrink, S., Cioromela, R., & Moldoveanu, F. (2012). GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations. In Proceedings of the 2012 IEEE 12th International Conference on Bioinformatics (pp. 251-254). IEEE (The Institute of Electrical and Electronics Engineers).
Huenenberger, P. H., Mark, A. E., & Berendsen, H. J. C. (2012). Wilfred van Gunsteren: 35 Years of Biomolecular Simulation. Journal of Chemical Theory and Computation, 8(10), 3425-3429. DOI: 10.1021/ct300692s
Goga, N., Rzepiela, A., de Sousa Pereira Simoes de Melo, M., de Vries, A., Hadar, A., Markvoort, A. J., ... Berendsen, H. (2012). Methods for multiscale modeling of membranes. In A. Iglic (Ed.), Advances in Planar Lipid Bilayers and Liposomes (pp. 139-170). Academic Press. DOI: 10.1016/B9780123965332000033
Wassenaar, T. A., de Vries, S., Bonvin, A. M. J. J., & Bekker, H. (2012). SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions. Journal of Chemical Theory and Computation, 8(10), 3618-3627. DOI: 10.1021/ct3000662
van Dijk, M., Wassenaar, T. A., & Bonvin, A. M. J. J. (2012). A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 8(10), 3463-3472. DOI: 10.1021/ct300102d

2011

Velinova, M., Sengupta, D., Tadjer, A. V., & Marrink, S-J. (2011). Sphere-to-Rod Transitions of Nonionic Surfactant Micelles in Aqueous Solution Modeled by Molecular Dynamics Simulations. Langmuir, 27(23), 14071-14077. DOI: 10.1021/la203055t
Sørensen, J., Periole, X., Skeby, K. K., Marrink, S-J., & Schiøtt, B. (2011). Protofibrillar Assembly Toward the Formation of Amyloid Fibrils. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2(19), 2385-2390. DOI: 10.1021/jz2010094
Klacsova, M., Bulacu, M., Kucerka, N., Uhrikova, D., Teixeira, J., Marrink, S. J., & Balgavy, P. (2011). The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles - A small-angle neutron scattering and molecular dynamics study. Biochimica et Biophysica Acta-Biomembranes, 1808(9), 2136-2146. DOI: 10.1016/j.bbamem.2011.04.010
Mika, J. T., Moiset, G., Cirac, A. D., Feliu, L., Bardaji, E., Planas, M., ... Poolman, B. (2011). Structural basis for the enhanced activity of cyclic antimicrobial peptides: The case of BPC194. Biochimica et Biophysica Acta-Biomembranes, 1808(9), 2197-2205. DOI: 10.1016/j.bbamem.2011.05.001
De Jong, D. H., Schafer, L. V., De Vries, A. H., Marrink, S. J., Berendsen, H. J. C., & Grubmueller, H. (2011). Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations. Journal of Computational Chemistry, 32(9), 1919-1928. DOI: 10.1002/jcc.21776
Fuhrmans, M., & Marrink, S-J. (2011). A tool for the morphological analysis of mixtures of lipids and water in computer simulations. Journal of Molecular Modeling, 17(7), 1755-1766. DOI: 10.1007/s00894-010-0858-6
Cirac, A. D., Moiset, G., Mika, J. T., Kocer, A., Salvador, P., Poolman, B., ... Sengupta, D. (2011). The Molecular Basis for Antimicrobial Activity of Pore-Forming Cyclic Peptides. Biophysical Journal, 100(10), 2422-2431. DOI: 10.1016/j.bpj.2011.03.057
Westerbeek, A., Szymanski, W., Wijma, H. J., Marrink, S., Feringa, B. L., & Janssen, D. B. (2011). Kinetic resolution of α-bromoamides: Experimental and theoretical investigation of highly enantioselective reactions catalyzed by haloalkane dehalogenases. Advanced Synthesis & Catalysis, 353(6), 931-944. DOI: 10.1002/adsc.201000726
Ollila, O. H. S., Louhivuori, M., Marrink, S. J., & Vattulainen, I. (2011). Protein Shape Change Has a Major Effect on the Gating Energy of a Mechanosensitive Channel. Biophysical Journal, 100(7), 1651-1659. DOI: 10.1016/j.bpj.2011.02.027
Risselada, H. J., Marrink, S. J., & Mueller, M. (2011). Curvature-Dependent Elastic Properties of Liquid-Ordered Domains Result in Inverted Domain Sorting on Uniaxially Compressed Vesicles. Physical Review Letters, 106(14), 148102-1-148102-4. [148102]. DOI: 10.1103/PhysRevLett.106.148102
Lopez, C. A., de Vries, A. H., & Marrink, S. J. (2011). Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction. PLoS Computational Biology, 7(3), e1002020-1-e1002020-1. [1002020]. DOI: 10.1371/journal.pcbi.1002020
Schaefer, L. V., de Jong, D. H., Holt, A., Rzepiela, A. J., de Vries, A. H., Poolman, B., ... Marrink, S. J. (2011). Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proceedings of the National Academy of Sciences of the United States of America, 108(4), 1343-1348. DOI: 10.1073/pnas.1009362108
Markvoort, A. J., & Marrink, S. J. (2011). Lipid Acrobatics in the Membrane Fusion Arena. In L. V. Chernomordik, & M. M. Kozlov (Eds.), Membrane Fusion (68 ed., pp. 259-294). (Current Topics in Membranes; Vol. 68). SAN DIEGO: Academic Press. DOI: 10.1016/B978-0-12-385891-7.00011-8
Rzepiela, A. J., Louhivuori, M., Peter, C., & Marrink, S. J. (2011). Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Physical Chemistry Chemical Physics, 13(22), 10437-10448. DOI: 10.1039/c0cp02981e
Murtola, T., Vuorela, T. A., Hyvonen, M. T., Marrink, S-J., Karttunen, M., & Vattulainen, I. (2011). Low density lipoprotein: structure, dynamics, and interactions of apoB-100 with lipids. Soft Matter, 7(18), 8135-8141. DOI: 10.1039/c1sm05367a
Berendsen, H. J. C. (2011). The Relevance of Distance Statistics for Protein Folding. Journal of Biomolecular Structure & Dynamics, 28(4), 599-601.
Millan-Pacheco, C., Saint-Martin, H., De Vries, A. H., & Ortega-Blake, I. (2011). Networking of sterols in lipid bilayers. European biophysics journal with biophysics letters, 40, 204.

2010

Schafer, L. V., & Marrink, S. J. (2010). Partitioning of Lipids at Domain Boundaries in Model Membranes. Biophysical Journal, 99(12), L91-L93. DOI: 10.1016/j.bpj.2010.08.072
Louhivuori, M., Risselada, H., Giessen, E. V. D., & Marrink, S. J. (2010). Release of content through mechano-sensitive gates in pressurized liposomes. Proceedings of the National Academy of Sciences of the United States of America, 107(46), 19856-19860. DOI: 10.1073/pnas.1001316107
Polyansky, A. A., Ramaswamy, R., Volynsky, P. E., Sbalzarini, I. F., Marrink, S. J., & Efremov, R. G. (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1(20), 3108-3111. DOI: 10.1021/jz101163e
Vuorela, T., Catte, A., Niemela, P. S., Hall, A., Hyvonen, M. T., Marrink, S-J., ... Vattulainen, I. (2010). Role of Lipids in Spheroidal High Density Lipoproteins. PLoS Computational Biology, 6(10), e1000964-1-e1000964-1. [1000964]. DOI: 10.1371/journal.pcbi.1000964
Ramadurai, S., Holt, A., Schafer, L. V., Krasnikov, V. V., Rijkers, D. T. S., Marrink, S. J., ... Poolman, B. (2010). Influence of Hydrophobic Mismatch and Amino Acid Composition on the Lateral Diffusion of Transmembrane Peptides. Biophysical Journal, 99(5), 1447-1454. DOI: 10.1016/j.bpj.2010.05.042
Kucerka, N., Marquardt, D., Harroun, T. A., Nieh, M. P., Wassall, S. R., de Jong , D. H., ... Katsaras, J. (2010). Cholesterol in Bilayers with PUFA Chains: Doping with DMPC or POPC Results in Sterol Reorientation and Membrane-Domain Formation. Biochemistry, 49(35), 7485-7493. DOI: 10.1021/bi100891z
Lycklama a Nijeholt, J. A., Bulacu, M., Marrink, S. J., & Driessen, A. J. M. (2010). Immobilization of the Plug Domain Inside the SecY Channel Allows Unrestricted Protein Translocation. The Journal of Biological Chemistry, 285(31), 23747 - 23754. DOI: 10.1074/jbc.M110.124636
Yesylevskyy, S. O., Schafer, L. V., Sengupta, D., & Marrink, S. J. (2010). Polarizable Water Model for the Coarse-Grained MARTINI Force Field. PLoS Computational Biology, 6(6), e1000810-1-e1000810-1. [1000810]. DOI: 10.1371/journal.pcbi.1000810
Smirnova, Y. G., Marrink, S-J., Lipowsky, R., & Knecht, V. (2010). Solvent-Exposed Tails as Prestalk Transition States for Membrane Fusion at Low Hydration. Journal of the American Chemical Society, 132(19), 6710-6718. DOI: 10.1021/ja910050x
Rzepiela, A. J., Schafer, L. V., Goga, N., Risselada, H. J., De Vries, A. H., & Marrink, S. J. (2010). Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures. Journal of Computational Chemistry, 31(6), 1333-1343. DOI: 10.1002/jcc.21415
Fuhrmans, M., Sanders, B. P., Marrink, S-J., & de Vries, A. H. (2010). Effects of bundling on the properties of the SPC water model. Theoretical Chemistry Accounts, 125(3-6), 335-344. DOI: 10.1007/s00214-009-0590-4
Baoukina, S., Marrink, S. J., & Tieleman, D. P. (2010). Lateral pressure profiles in lipid monolayers. Faraday Discussions, 144(8), 393-409. DOI: 10.1039/b905647e
Apajalahti, T., Niemela, P., Govindan, P. N., Miettinen, M. S., Salonen, E., Marrink, S-J., & Vattulainen, I. (2010). Concerted diffusion of lipids in raft-like membranes. Faraday Discussions, 144, 411-430. DOI: 10.1039/b901487j
Rzepiela, A. J., Sengupta, D., Goga, N., & Marrink, S. J. (2010). Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions. Faraday Discussions, 144(12), 431-443. DOI: 10.1039/b901615e
Marrink, S. J., Periole, X., Tieleman, D. P., & de Vries, A. H. (2010). Comment on "On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models'' by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934. Physical Chemistry Chemical Physics, 12(9), 2254-2256. DOI: 10.1039/b915293h
Sengupta, D., & Marrink, S. J. (2010). Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes. Physical Chemistry Chemical Physics, 12(40), 12987-12996. DOI: 10.1039/c0cp00101e
Berendsen, H. J. C. (2010). Concluding Remarks. Faraday Discussions, 144, 467 - 481.
Horta, B. A. C., de Vries, A. H., & Hunenberger, P. H. (2010). Simulating the Transition between Gel and Liquid-Crystal Phases of Lipid Bilayers: Dependence of the Transition Temperature on the Hydration Level. Journal of Chemical Theory and Computation, 6(8), 2488-2500. DOI: 10.1021/ct100200w

2009

Hinner, M. J., Marrink, S-J., & de Vries, A. H. (2009). Location, Tilt, and Binding: A Molecular Dynamics Study of Voltage-Sensitive Dyes in Biomembranes. Journal of Physical Chemistry B, 113(48), 15807-15819. DOI: 10.1021/jp907981y
Sengupta, D., Rampioni, A., & Marrink, S-J. (2009). Simulations of the c-subunit of ATP-synthase reveal helix rearrangements. Molecular Membrane Biology, 26(8), 422-434. DOI: 10.3109/09687680903321073
Lopez, C. A., Rzepiela, A. J., de Vries, A. H., Dijkhuizen, L., Huenenberger, P. H., & Marrink, S. J. (2009). Martini Coarse-Grained Force Field: Extension to Carbohydrates. Journal of Chemical Theory and Computation, 5(12), 3195-3210. DOI: 10.1021/ct900313w
Esteban-Martin, S., Risselada, H. J., Salgado, J., & Marrink, S. J. (2009). Stability of asymmetric lipid bilayers assessed by molecular dynamics simulations. Journal of the American Chemical Society, 131(42), 15194-15202. DOI: 10.1021/ja904450t
Lee, H., de Vries, A. H., Marrink, S-J., & Pastor, R. W. (2009). A Coarse-Grained Model for Polyethylene Oxide and Polyethylene Glycol: Conformation and Hydrodynamics. Journal of Physical Chemistry B, 113(40), 13186-13194. DOI: 10.1021/jp9058966
Kucerka, N., Gallova, J., Uhrikova, D., Balgavy, P., Bulacu, M. I., Marrink, S. J., & Katsaras, J. (2009). Areas of monounsaturated diacylphosphatidylcholines. Biophysical Journal, 97(7), 1926-1932. DOI: 10.1016/j.bpj.2009.06.050
Bennett, W. F. D., MacCallum, J. L., Hinner, M. J., Marrink, S. J., & Tieleman, D. P. (2009). Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments. Journal of the American Chemical Society, 131(35), 12714-12720. DOI: 10.1021/ja903529f
Periole, X., Cavalli, M., Marrink, S-J., & Ceruso, M. A. (2009). Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. Journal of Chemical Theory and Computation, 5(9), 2531-2543. DOI: 10.1021/ct9002114
Goga, N., Costache, S., & Marrink, S. (2009). New Gromacs Implementations for Multiscaling Space MD. Materiale Plastice, 46(3), 220-223.
Masman, M. F., Eisel, U. L. M., Csizmadia, I. G., Penke, B., Enriz, R. D., Marrink, S. J., & Luiten, P. G. M. (2009). In Silico Study of Full-Length Amyloid β 1-42 Tri- and Penta-Oligomers in Solution. Journal of Physical Chemistry B., 113(34), 11710-11719. DOI: 10.1021/jp901057w
Fuhrmans, M., Knecht, V., & Marrink, S. J. (2009). A Single Bicontinuous Cubic Phase Induced by Fusion Peptides. Journal of the American Chemical Society, 131(26), 9166-+. DOI: 10.1021/ja903224q
Yesylevskyy, S., Marrink, S-J., & Mark, A. E. (2009). Alternative Mechanisms for the Interaction of the Cell-Penetrating Peptides Penetratin and the TAT Peptide with Lipid Bilayers. Biophysical Journal, 97(1), 40-49. DOI: 10.1016/j.bpj.2009.03.059
Berntsson, R. P-A., Doeven, M. K., Fusetti, F., Duurkens, R. H., Sengupta, D., Marrink, S-J., ... Slotboom, D-J. (2009). The structural basis for peptide selection by the transport receptor OppA. EMBO Journal, 28(9), 1332-1340. DOI: 10.1038/emboj.2009.65
Siwko, M. E., de Vries, A. H., Mark, A. E., Kozubek, A., & Marrink, S. J. (2009). Disturb or Stabilize? A Molecular Dynamics Study of the Effects of Resorcinolic Lipids on Phospholipid Bilayers. Biophysical Journal, 96(8), 3140-3153. DOI: 10.1016/j.bpj.2009.01.040
Ollila, O. H. S., Risselada, H. J., Louhivuori, M., Lindahl, E., Vattulainen, I., & Marrink, S. J. (2009). 3D Pressure Field in Lipid Membranes and Membrane-Protein Complexes. Physical Review Letters, 102(7), [078101]. DOI: 10.1103/physrevlett.102.078101
Marrink, S. J., de Vries, A. H., & Tieleman, D. P. (2009). Lipids on the move: Simulations of membrane pores, domains, stalks and curves. Biochimica et Biophysica Acta-Biomembranes, 1788(1), 149-168. DOI: 10.1016/j.bbamem.2008.10.006
Risselada, H. J., & Marrink, S. J. (2009). Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations. Physical Chemistry Chemical Physics, 11(12), 2056-2067. DOI: 10.1039/b818782g
Baoukina, S., Marrink, S. J., & Tieleman, D. P. (2009). Structure and dynamics of lipid monolayers: theory and applications. In Editor Thomas Jue (Ed.), Biomembrane Frontiers (pp. 75 - 99). (HANDBOOK OF MODERN BIOPHYSICS Series). Humana Press.
Goga, N., Costache, S., & Marrink, S. (2009). A Multiscalling Constant Lambda Molecular Dynamic Gromacs Implementation. Materiale Plastice, 46(1), 53-57.
Risselada, H. J., & Marrink, S. J. (2009). The freezing process of small lipid vesicles at molecular resolution. Soft Matter, 5(22), 4531-4541. DOI: 10.1039/b913210d
Louhivuori, M., Risselada, J., Giessen, E. V. D., & Marrink, S-J. (2009). MscL Gating In Liposomes. 254a-254a.
Winger, M., de Vries, A. H., & van Gunsteren, W. F. (2009). Force-field dependence of the conformational properties of ,-dimethoxypolyethylene glycol. Molecular Physics, 107(13), 1313-1321. [911054506]. DOI: 10.1080/00268970902794826
Wassenaar, T. A., Daura, X., Padros, E., & Mark, A. E. (2009). Calcium binding to the purple membrane: A molecular dynamics study. Proteins, 74(3), 669-681. DOI: 10.1002/prot.22182

2008

Risselada, H. J., & Marrink, S. J. (2008). The molecular face of lipid rafts in model membranes. Proceedings of the National Academy of Sciences of the United States of America, 105(45), 17367-17372. DOI: 10.1073/pnas.0807527105
Sengupta, D., Leontiadou, H., Mark, A. E., & Marrink, S-J. (2008). Toroidal pores formed by antimicrobial peptides show significant disorder. Biochimica et Biophysica Acta-Biomembranes, 1778(10), 2308-2317. DOI: 10.1016/j.bbamem.2008.06.007
Baoukina, S., Monticelli, L., Risselada, H. J., Marrink, S. J., & Tieleman, D. P. (2008). The molecular mechanism of lipid monolayer collapse. Proceedings of the National Academy of Sciences of the United States of America, 105(31), 10803-10808. DOI: 10.1073/pnas.0711563105
Risselada, H. J., Mark, A. E., & Marrink, S. J. (2008). Application of mean field boundary potentials in simulations of lipid vesicles. Journal of Physical Chemistry B, 112(25), 7438-7447. DOI: 10.1021/jp0758519
Monticelli, L., Kandasamy, S. K., Periole, X., Larson, R. G., Tieleman, D. P., & Marrink, S-J. (2008). The MARTINI coarse-grained force field: Extension to proteins. Journal of Chemical Theory and Computation, 4(5), 819-834. DOI: 10.1021/ct700324x
Yefimov, S., Giessen, E. V. D., Onck, P. R., & Marrink, S. J. (2008). Mechanosensitive membrane channels in action. Biophysical Journal, 94(8), 2994-3002. DOI: 10.1529/biophysj.107.119966
Treptow, W., Marrink, S. J., & Tarek, M. (2008). Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. Journal of Physical Chemistry B., 112(11), 3277-3282. DOI: 10.1021/jp709675e
Catte, A., Patterson, J. C., Bashtovyy, D., Jones, M. K., Gu, F., Li, L., ... Segrest, J. P. (2008). Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations. Biophysical Journal, 94(6), 2306-2319. DOI: 10.1529/biophysj.107.115857
Knecht, V., Risselada, H. J., Mark, A. E., & Marrink, S. J. (2008). Electrophoretic mobility does not always reflect the charge on an oil droplet. Journal of Colloid and Interface Science, 318(2), 477-486. DOI: 10.1016/j.jcis.2007.10.035
Marrink, S. J., de Vries, A. H., Harroun, T. A., Katsaras, J., & Wassall, S. R. (2008). Cholesterol shows preference for the interior of polyunsaturated lipid. Journal of the American Chemical Society, 130(1), 10 - 11. DOI: 10.1021/ja076641c
Marrink, S. J., Fuhrmans, M., Risselada, H. J., & Periole, X. (2008). The MARTINI force field. In G. Voth (Ed.), Coarse graining of condensed phase and biomolecular systems (pp. 2). CRC Press.
Wassenaar, T. A., Quax, W. J., & Mark, A. E. (2008). The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: A molecular dynamics study. Proteins-Structure Function and Bioinformatics, 70(2), 333-343. DOI: 10.1002/prot.21541

2007

Baoukina, S., Monticelli, L., Marrink, S. J., & Tieleman, D. P. (2007). Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir, 23(25), 12617-12623. DOI: 10.1021/la702286h
Periole, X., Huber, T., Marrink, S-J., & Sakmar, T. P. (2007). G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. Journal of the American Chemical Society, 129(33), 10126-10132. DOI: 10.1021/ja0706246
Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H. (2007). The MARTINI force field: Coarse grained model for biomolecular simulations. Journal of Physical Chemistry B, 111(27), 7812-7824. DOI: 10.1021/jp071097f
Leontiadou, H., Mark, A. E., & Marrink, S-J. (2007). Ion transport across transmembrane pores. Biophysical Journal, 92(12), 4209-4215. DOI: 10.1529/biophysj.106.101295
Knecht, V., & Marrink, S-J. (2007). Molecular dynamics simulations of lipid vesicle fusion in atomic detail. Biophysical Journal, 92(12), 4254-4261. DOI: 10.1529/biophysj.106.103572
Siwko, M. E., Marrink, S. J., de Vries, A. H., Arkadiusz, K., Schoot Uiterkamp, A. J. M., & Mark, A. E. (2007). Does isoprene protect plant membranes for thermal shock? A molecular dynamics study. Biochimica et Biophysica Acta-Biomembranes, 1768(2), 198-206. DOI: 10.1016/j.bbamem.2006.09.023
Catte, A., Patterson, J. C., Bashtovyy, D., Jones, M. K., Gu, F. F., Li, L., ... Segrest, J. P. (2007). Preliminary models of spheroidal HDL particles through molecular dynamics. Biophysical Journal, 539A.
Baron, R., Trzesniak, D., de Vries, A. H., Elsener, A., Marrink, S. J., & van Gunsteren, W. F. (2007). Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. Chemphyschem, 8(3), 452 - 461. DOI: 10.1002/cphc.200600658
de Vries, A. H., Fuhrmans, M., Risselada, H. J., Siwko, M. E., Knecht, V., & Marrink, S. J. (2007). Phase transformations of lipid aggregates at molecular resolution. Biophysical Journal, (Suppl. S), 192A-193A.
van den Bogaart, G., Hermans, N., Krasnikov, V., de Vries, A. H., & Poolman, B. (2007). On the decrease in lateral mobility of phospholipids by sugars. Biophysical Journal, 92(5), 1598-1605. DOI: 10.1529/biophysj.106.096461
Villa, A., Fan, H., Wassenaar, T., & Mark, A. E. (2007). How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field? Journal of Physical Chemistry B, 111(21), 6015-6025. DOI: 10.1021/jp068580v

2006

Tieleman, D. P., & Marrink, S-J. (2006). Lipids out of equilibrium: Energetics of desorption and pore mediated flip-flop. Journal of the American Chemical Society, 128(38), 12462-12467. DOI: 10.1021/ja0624321
Leontiadou, H., Mark, A. E., & Marrink, S. J. (2006). Antimicrobial peptides in action. Journal of the American Chemical Society, 128(37), 12156-12161. DOI: 10.1021/ja062927q
Knecht, V., Mark, A. E., & Marrink, S-J. (2006). Phase Behavior of a Phospholipid/Fatty Acid/Water Mixture Studied in Atomic Detail. Journal of the American Chemical Society, 128(6), 2030 - 2034. DOI: 10.1021/ja056619a
Hozoi, L., de Vries, A. H., Broer, R., de Graaf, C., & Bagus, P. S. (2006). Ni 3s-hole states in NiO by non-orthogonal configuration interaction. Chemical Physics, 331(1), 178-185. DOI: 10.1016/j.chemphys.2006.10.015
Baron, R., de Vries, A. H., Huenenberger, P. H., & van Gunsteren, W. F. (2006). Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. Journal of Physical Chemistry B, 110(31), 15602-15614. DOI: 10.1021/jp061627s
Baron, R., de Vries, A. H., Hunenberger, P. H., & van Gunsteren, W. F. (2006). Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. Journal of Physical Chemistry B, 110(16), 8464-8473. DOI: 10.1021/jp055888y
Wassenaar, T. A. (2006). Molecular dynamics of sense and sensibility in processing and analysis of data s.n.

2005

Marrink, S. J., Risselada, J., & Mark, A. E. (2005). Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chemistry and Physics of Lipids, 135(2), 223-244. DOI: 10.1016/j.chemphyslip.2005.03.001
de Vries, A. H., Yefimov, S., Mark, A. E., & Marrink, S. J. (2005). Molecular structure of the lecithin ripple phase. Proceedings of the National Academy of Sciences of the United States of America, 102(15), 5392-5396. DOI: 10.1073/pnas.0408249102
Knecht, V., Muller, M., Bonn, M., Marrink, S. J., & Mark, A. E. (2005). Simulation studies of pore and domain formation in a phospholipid monolayer. Journal of Chemical Physics, 122(2), 24704 - 24713. [024704]. DOI: 10.1063/1.1825992
van den Bosch, M., Swart, M., Snijders, J. G., Berendsen, H. J. C., Mark, A. E., Oostenbrink, C., ... Canters, G. W. (2005). Calculation of the redox potential of the protein azurin and some mutants. ChemBioChem, 6(4), 738-746. DOI: 10.1002/cbic.200400244
van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701 - 1718. DOI: 10.1002/jcc.20291
de Vries, A. H., Chandrasekhar, I., van Gunsteren, W. F., Hunenberger, P. H., & Chandrasekhar, . N. V. (2005). Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time: Influence of artificial periodicity, system size, and simulation time. Journal of Physical Chemistry B, 109(23), 11643-11652. DOI: 10.1021/jp0507952

2004

de Vries, A. H., Mark, A. E., & Marrink, S. J. (2004). Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail. Journal of the American Chemical Society, 126(14), 4488-4489. DOI: 10.1021/ja0398417
Leontiadou, H., Mark, A. E., & Marrink, S. J. (2004). Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers. Biophysical Journal, 86(4), 2156-2164. DOI: 10.1016/S0006-3495(04)74275-7
de Vries, A. H., Mark, A. E., & Marrink, S. J. (2004). The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics study. Journal of Physical Chemistry B, 108(7), 2454-2463. DOI: 10.1021/jp0366926
Marrink, S. J., de Vries, A. H., & Mark, A. E. (2004). Coarse grained model for semiquantitative lipid simulations. Journal of Physical Chemistry B, 108(2), 750-760. DOI: 10.1021/jp036508g
Marrink, S. J., & Mark, A. E. (2004). Molecular view of hexagonal phase formation in phospholipid membranes. Biophysical Journal, 87(6), 3894 - 3900. DOI: 10.1529/biophysj.104.048710
Faller, R., & Marrink, S. J. (2004). Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir, 20(18), 7686 - 7693. DOI: 10.1021/la0492759
Marrink, S. J. (2004). Molecular dynamics simulation of cholesterol nucleation in mixed micelles modelling human bile. In G. Adler, M. Fuchs, H. E. Blum, & E. F. Stange (Eds.), GALLSTONES: PATHOGENESIS AND TREATMENT (pp. 98-105 - 13). (FALK SYMPOSIUM; Vol. 139). DORDRECHT: Kluwer Academic Publishers.
Rispens, T., Lensink, M. F., Berendsen, H. J. C., & Engberts, J. B. F. N. (2004). Molecular dynamics simulation of the effect of hydrophobic cosolutes on the neutral hydrolysis of an activated ester. Journal of Physical Chemistry B, 108(17), 5483-5488. DOI: 10.1021/jp037120o
Groenhof, G., Bouxin-Cademartory, M., Hess, B., De Visser, S. P., Berendsen, H. J. C., Olivucci, M., ... Robb, M. A. (2004). Photoactivation of the photoactive yellow protein: Why photon absorption triggers a trans-to-cis lsomerization of the chromophore in the protein. Journal of the American Chemical Society, 126(13), 4228-4233. DOI: 10.1021/ja039557f
Saint-Martin, H., Hess, B., & Berendsen, H. J. C. (2004). An application of flexible constraints in Monte Carlo simulations of the isobaric-isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model. Journal of Chemical Physics, 120(23), 11133 - 11143. DOI: 10.1063/1.1747927
Smith, L. J., Berendsen, H. J. C., & van Gunsteren, W. F. (2004). Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation: A test of force field parameters for use in biomolecular simulation. Journal of Physical Chemistry B, 108(3), 1065 - 1071. DOI: 10.1021/jp030534x
Folgering, J. H. A., Kuiper, J. M., Vries, A. H. D., Engberts, J. B. F. N., & Poolman, B. (2004). Lipid-Mediated Light Activation of a Mechanosensitive Channel of Large Conductance. Langmuir, 20(17), 6985 - 6987. DOI: 10.1021/la048942v
Bekker, H., Van den Berg, J. P., & Wassenaar, T. A. (2004). A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints. Journal of Computational Chemistry, 25(8), 1037-1046. DOI: 10.1002/jcc.20050

2003

Marrink, S. J., & Mark, A. E. (2003). Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. Journal of the American Chemical Society, 125(49), 15233-15242. DOI: 10.1021/ja0352092
Marrink, S. J., & Mark, A. E. (2003). The mechanism of vesicle fusion as revealed by molecular dynamics simulations. Journal of the American Chemical Society, 125(37), 11144-11145. DOI: 10.1021/ja036138+
Anezo, C., de Vries, A. H., Holtje, H. D., Tieleman, D. P., & Marrink, S. J. (2003). Methodological issues in lipid bilayer simulations. Journal of Physical Chemistry B, 107(35), 9424-9433. DOI: 10.1021/jp0348981
Tieleman, D. P., Leontiadou, H., Mark, A. E., & Marrink, S. J. (2003). Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. Journal of the American Chemical Society, 125(21), 6382-6383. DOI: 10.1021/ja029504i
Colombo, G., Marrink, S. J., & Mark, A. E. (2003). Simulation of MscL Gating in a bilayer under stress. Biophysical Journal, 84(4), 2331-2337. DOI: 10.1016/S0006-3495(03)75038-3
Berendsen, H. J. C. (2003). Inter-union bioinformatics group report. Acta Crystallographica Section D: Biological Crystallography, 59, 777-782. DOI: 10.1107/S0807444903000805
de Vries, A. H., Hozoi, L., & Broer, R. (2003). Origin of the chemical shift in X-ray absorption near-edge spectroscopy at the Mn K-Edge in manganese oxide compounds. International Journal of Quantum Chemistry, 91(1), 57-61. DOI: 10.1002/qua.10370
Bekker, H., van den Berg, J. P., & Wassenaar, T. A. (2003). Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions. In EPRINTS-BOOK-TITLE Springer.

2002

van Eijk, M. C. P., Bergsma, M., & Marrink, S. J. (2002). Association behaviour of glucitol amine gemini surfactants - Self-consistent-field theory and molecular-dynamics simulations. European Physical Journal E, 7(4), 317-324. DOI: 10.1140/epje/i2002-10012-6
Marrink, S. J., & Mark, A. E. (2002). Molecular dynamics simulations of mixed micelles modeling human bile. Biochemistry, 41(17), 5375 - 5382. DOI: 10.1021/bi015613i
Marrink, S. J., & Tieleman, D. P. (2002). Molecular dynamics simulation of spontaneous membrane fusion during a cubic-hexagonal phase transition. Biophysical Journal, 83(5), 2386 - 2392. DOI: 10.1016/S0006-3495(02)75252-1
Garnier, J., & Berendsen, H. J. C. (2002). International unions concerned about biodata - Action must be taken now to ensure that data are safely archived and always accessible. Nature, 419(6909), 777-777.
Flohil, J. A., Vriend, G., & Berendsen, H. J. C. (2002). Completion and refinement of 3-D homology models with restricted molecular dynamics: Application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis: Application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis. Proteins-Structure Function and Genetics, 48(4), 593 - 604. DOI: 10.1002/prot.10105
Groenhof, G., Lensink, M. F., Berendsen, H. J. C., & Mark, A. E. (2002). Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes. Proteins-Structure Function and Genetics, 48(2), 212 - 219. DOI: 10.1002/prot.10135
Hess, B., Saint-Martin, H., & Berendsen, H. J. C. (2002). Flexible constraints: An adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable mobile charge densities in harmonic oscillators model for water: An adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable mobile charge densities in harmonic oscillators model for water. Journal of Chemical Physics, 116(22), 9602 - 9610. DOI: 10.1063/1.1478056
Pikkemaat, M. G., Linssen, A. B. M., Berendsen, H. J. C., & Janssen, D. B. (2002). Molecular dynamics simulations as a tool for improving protein stability. Protein Engineering, 15(3), 185 - 192. DOI: 10.1093/protein/15.3.185
van den Berg, P. A. W., Feenstra, K. A., Mark, A. E., Berendsen, H. J. C., & Visser, A. J. W. G. (2002). Dynamic conformations of flavin adenine dinucleotide: Simulated molecular dynamics of the flavin cofactor related to the time-resolved fluorescence characteristics. Journal of Physical Chemistry B, 106(34), 8858-8869. DOI: 10.1021/jp020356s
van Lune, F., Manning, L., Dijkstra, K., Berendsen, H. J. C., & Scheek, R. M. (2002). Order-parameter tensor description of HPr in a medium of oriented bicelles. Journal of Biomolecular Nmr, 23(3), 169 - 179.
Groenhof, G., Lensink, M. F., Berendsen, H. J. C., Snijders, J. G., & Mark, A. E. (2002). Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore. Proteins-Structure Function and Genetics, 48(2), 202 - 211. DOI: 10.1002/prot.10136
Hozoi, L., de Vries, A. H., van Oosten, A. B., Broer-Braam, H. B., Cabrero, J., & Graaf, de, C. (2002). Theoretical characterization of the ground and optically excited states of alpha '-NaV2O5. Physical Review Letters, 89(7), [076407]. DOI: 10.1103/physrevlett.89.076407
van Duijnen, P. T., de Vries, A. H., de Swart, M., & Grozema, F. C. (2002). Polarizabilities in the condensed phase and the local fields problem: A direct reaction field formulation: A direct reaction field formulation. Journal of Chemical Physics, 117(18), 8442 - 8453. DOI: 10.1063/1.1512278
de Vries, A. H., Hozoi, L., Broer, R., & Bagus, P. S. (2002). Importance of interatomic hole screening in core-level spectroscopy of transition metal oxides: Mn 3s hole states in MnO. Physical Review B, 66(3), [035108]. DOI: 10.1103/PhysRevB.66.035108

2001

Marrink, S. J., & Mark, A. E. (2001). Effect of Undulations on Surface Tension in Simulated Bilayers. The Journal of Physical Chemistry B, 105(26), 6122 - 6127. DOI: 10.1021/jp0103474
Marrink, S. J., & Tieleman, D. P. (2001). Molecular dynamics simulation of a lipid diamond cubic phase. Journal of the American Chemical Society, 123(49), 12383 - 12391. DOI: 10.1021/ja016012h
Marrink, S. J., Lindahl, E., Edholm, O., & Mark, A. E. (2001). Simulation of the spontaneous aggregation of phospholipids into bilayers. Journal of the American Chemical Society, 123(35), 8638 - 8639. DOI: 10.1021/ja0159618
Marrink, S-J., & Marčelja, S. (2001). Potential of Mean Force Computations of Ions Approaching a Surface. Langmuir, 17(25). DOI: 10.1021/la015526r
Knackstedt, M. A., Marrink, S. J., Sheppard, A. P., Pinczewski, W. V., & Sahimi, M. (2001). Invasion Percolation on Correlated and Elongated Lattices: Implications for the Interpretation of Residual Saturations in Rock Cores. Transport in Porous Media, 44(3). DOI: 10.1023/A:1010770010309
Berendsen, H. J. C. (2001). Bioinformatics - Reality simulation - Observe while it happens. Science, 294(5550), 2304 - 2305. DOI: 10.1126/science.1067546
Berendsen, H. J. C. (2001). Slow events in complex systems: potentials of mean form and the Smoluchokowski limit in biological systems. SIMU Newsletter, MODYN(3), 33 - 50.
Choma, C. T., Tieleman, D. P., Cregut, D., Serrano, L., & Berendsen, H. J. C. (2001). Towards the design and computational characterization of a membrane protein. Journal of Molecular Graphics & Modelling, 20(3), 219 - 234.
Creveld, L. D., Meijberg, W., Berendsen, H. J. C., & Pepermans, H. A. M. (2001). DSC studies of Fusarium solani pisi cutinase: consequences for stability in the presence of surfactants: consequences for stability in the presence of surfactants. Biophysical Chemistry, 92(1-2), 65 - 75.
Tieleman, D. P., Berendsen, H. J. C., & Sansom, M. S. P. (2001). Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces. Biophysical Journal, 80(1), 331 - 346.
de Swart, M., Van den Bosch, M., Berendsen, H. J. C., Canters, G. W., & Snijders, J. G. (2001). Density functional theory and molecular dynamics results for copper proteins. Journal of Inorganic Biochemistry, 86(1), 445 - 445.
Hozoi, L., de Vries, A. H., & Broer-Braam, H. B. (2001). X-ray spectroscopy at the MnK edge in LaMnO3: An ab initio study. Physical Review B, 6416(16), [165104]. DOI: 10.1103/PhysRevB.64.165104
Hozoi, L., Vries, A. H. D., & Broer, R. (2001). X-ray spectroscopy at the Mn K edge in LaMnO3: An ab initio study. Physical Review B, 64(16). DOI: 10.1103/PhysRevB.64.165104

2000

Marrink, S. J., Tieleman, D. P., & Mark, A. E. (2000). Molecular dynamics simulation of the kinetics of spontaneous micelle formation. Journal of Physical Chemistry B, 104(51), 12165 - 12173. DOI: 10.1021/jp001898h
Marrink, S. J., Paterson, L., & Knackstedt, M. A. (2000). Definition of percolation thresholds on self-affine surfaces. Physica A: Statistical Mechanics and its Applications, 280(3). DOI: 10.1016/S0378-4371(99)00608-1
Marrink, S. J., & Knackstedt, M. A. (2000). Finite size scaling for percolation on elongated lattices in two and three dimensions. Physical Review E, 62(3). DOI: 10.1103/PhysRevE.62.3205
Saint-Martin, H., Hernandez-Cobos, J., Bernal-Uruchurtu, M. I., Ortega-Blake, . N. V., & Berendsen, H. J. C. (2000). A mobile charge densities in harmonic oscillators (MCDHO) molecular model for numerical simulations: The water-water interaction. Journal of Chemical Physics, 113(24), 10899-10912. [PII [S0021-9606(00)50847-2]].
Wensink, E. J. W., Hoffmann, A. C., Apol, M. E. F., & Berendsen, H. J. C. (2000). Properties of adsorbed water layers and the effect of adsorbed layers on interparticle forces by liquid bridging. Langmuir, 16(19), 7392-7400. DOI: 10.1021/la000009e
Berendsen, H. J. C., & Hayward, S. (2000). Collective protein dynamics in relation to function. Current Opinion in Structural Biology, 10(2), 165 - 169.
Tieleman, D. P., van der Spoel, D., & Berendsen, H. J. C. (2000). Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: Micellar structure and chain relaxation: Micellar structure and chain relaxation. Journal of Physical Chemistry B, 104(27), 6380 - 6388.

1999

Marrink, S. J., & Knackstedt, M. A. (1999). Percolation thresholds on elongated lattices. Journal of Physics A%3A Mathematical and General, 32(44). DOI: 10.1088/0305-4470/32/44/101
Lensink, M. F., Mavri, J., & Berendsen, H. J. C. (1999). Simulation of slow reaction with quantum character: Neutral hydrolysis of carboxylic ester. Journal of Computational Chemistry, 20(8), 886-895.
Amadei, A., de Groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A., & Berendsen, H. J. C. (1999). A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells: Diffusion between multiple harmonic wells. Proteins-Structure Function and Genetics, 35(3), 283 - 292.
Amadei, A., Apol, M. E. F., Chillemi, G., Berendsen, H. J. C., & Di Nola, A. (1999). Derivation of a general fluid equation of state based on the quasi-Gaussian entropy theory: application to the Lennard-Jones fluid: application to the Lennard-Jones fluid. Molecular Physics, 96(10), 1469 - 1490.
Apol, M. E. F., Amadei, A., Berendsen, H. J. C., & Di Nola, A. (1999). Derivation of thermal equations of state for quantum systems using the quasi-Gaussian entropy theory. Journal of Chemical Physics, 111(10), 4431 - 4441.
de Groot, B. L., Vriend, G., & Berendsen, H. J. C. (1999). Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism: New insights into the allosteric mechanism. Journal of Molecular Biology, 286(4), 1241 - 1249.
Feenstra, K. A., Hess, B., & Berendsen, H. J. C. (1999). Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. Journal of Computational Chemistry, 20(8), 786 - 798.
Kouwijzer, M. L. C. E., Berendsen, H. J. C., & Grootenhuis, P. D. J. (1999). Computer simulations of the dynamics of human choriogonadotropin and its alpha subunit. Proteins-Structure Function and Genetics, 37(4), 668 - 682.
Roccatano, D., Amadei, A., Di Nola, A., & Berendsen, H. J. C. (1999). A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G. Protein Science, 8(10), 2130 - 2143. DOI: 10.1110/ps.8.10.2130
Sansom, M. S. P., Tieleman, D. P., & Berendsen, H. J. C. (1999). Alamethicin: Molecular dynamics simulations of a channel- forming peptide: Molecular dynamics simulations of a channel-forming peptide. Biophysical Journal, 76(1), A444 - A444.
Tieleman, D. P., Sansom, M. S. P., & Berendsen, H. J. C. (1999). Alamethicin helices in a bilayer and in solution: Molecular dynamics simulations: Molecular dynamics simulations. Biophysical Journal, 76(1), 40 - 49.
Tieleman, D. P., Berendsen, H. J. C., & Sansom, M. S. P. (1999). An alamethicin channel in a lipid bilayer: Molecular dynamics simulations: Molecular dynamics simulations. Biophysical Journal, 76(4), 1757 - 1769.
Tieleman, D. P., Choma, C. T., & Berendsen, H. J. C. (1999). The use of molecular dynamics in De Novo design: application to a transmembrane four-helix coiled coil: application to a transmembrane four-helix coiled coil. Biophysical Journal, 76(1), A426 - A426.
Tieleman, D. P., Berendsen, H. J. C., & Sansom, M. S. P. (1999). Surface binding of alamethicin stabilizes its helical structure: Molecular dynamics simulations: Molecular dynamics simulations. Biophysical Journal, 76(6), 3186 - 3191.
de Vries, A. H., Sherwood, P., Collins, S. J., Rigby, A. M., Rigutto, M., & Kramer, G. J. (1999). Zeolite structure and reactivity by combined quantum-chemical- classical calculations. Journal of Physical Chemistry B, 103(29), 6133 - 6141.

1998

Marrink, S-J., Berger, O., Tieleman, P., & Jähnig, F. (1998). Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophysical Journal, 74(2), 931-943. DOI: 10.1016/s0006-3495(98)74016-0
Berendsen, H. J. C. (1998). A Glimpse of the Holy Grail? Science, 282, 642 - 643.
Tieleman, D. P., Forrest, L. R., Sansom, M. S. P., & Berendsen, H. J. C. (1998). Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations: Molecular dynamics simulations. Analytical Biochemistry, 37(50), 17554 - 17561.
Tieleman, D. P., Forest, L. R., Sansom, M. S. P., & Berendsen, H. J. C. (1998). Molecular dynamics simulations of membranes with embedded ion channels: porin, alamethicin and influenza M2. Biochem. Soc. Transac., 26, 438 - 443.
Veltman, O. R., Vriend, G., Berendsen, H. J. C., van den Burg, B., Venema, G., & Eijsink, V. G. H. (1998). A single calcium binding site is crucial for the calcium dependent thermal stability of thermolysin-like proteases. Biochemistry, 37(15), 5312-5319.
Apol, M. E. F., Amadei, A., & Berendsen, H. J. C. (1998). On the use of the quasi-Gaussian entropy theory in non-canonical ensembles. II. Prediction of density dependence of thermodynamic properties. Journal of Chemical Physics, 109, 3018 - 3027.
Creveld, L. D., Amadei, A., van Schaik, C., Pepemans, H. A. M., Vlieg, J., & Berendsen, H. J. C. (1998). Identification of functional and unfolding motions of cutinases as obtained from molecular dynamics coputer simulations. Proteins, 33, 253 - 264.
Amadei, A., Apol, M. E. F., & Berendsen, H. J. C. (1998). On the use of the quasi-Gaussian entropy theory in non-canonial ensembles. I. Prediction of temperature dependence of thermodynamic properties. Journal of Chemical Physics, 109, 3004 - 3016.
Tieleman, D. P., & Berendsen, H. J. C. (1998). A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated POPE bilayer. Biophysical Journal, 74(6), 2786 - 2801. DOI: 10.1016/S0006-3495(98)77986-X
de Groot, B. L., Hayward, S. J., Aalten, D. M. F., Amadei, A., & Berendsen, H. J. C. (1998). Domain motions in bacteriophage T4 lysozyme; a comparison between molecular dynamics and crystallographic data. Proteins, 31, 116 - 127.
Hayward, S., & Berendsen, H. J. C. (1998). Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme: New results on citrate synthase and T4 lysozyme. Proteins-Structure Function and Genetics, 30(2), 144 - 154.
Vriend, G., Berendsen, H. J. C., van den Burg, B., Venema, G., & Eijsink, V. G. H. (1998). Early steps in the unfolding of thermoysin-like proteases. The Journal of Biological Chemistry, 273, 35074 - 35077.
Berendsen, H. J. C., & Tieleman, D. P. (1998). Molecular dynamics: studies of lipid bilayers. New York: Wiley.
Amadei, A., Apol, M. E. F., & Berendsen, H. J. C. (1998). On the use of the quasi-Gaussian entropy theory in noncanonical ensembles. I. Prediction of temperature dependence of thermodynamic properties. Journal of Chemical Physics, 109(8), 3004 - 3016.
Apol, M. E. F., Amadei, A., & Berendsen, H. J. C. (1998). On the use of the quasi-Gaussian entropy theory in noncanonical ensembles. II. Prediction of density dependence of thermodynamic properties. Journal of Chemical Physics, 109(8), 3017 - 3027.
Berendsen, H. J. C. (1998). Protein folding - A glimpse of the holy grail? Science, 282(5389), 642 - 643.
Creveld, L. D., Amadei, A., van Schaik, R. C., Pepermans, H. A. M., de Vlieg, J., & Berendsen, H. J. C. (1998). Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations. Proteins-Structure Function and Genetics, 33(2), 253 - 264.
de Groot, B. L., Hayward, S., van Aalten, D. M. F., Amadei, A., & Berendsen, H. J. C. (1998). Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data: A comparison between molecular dynamics and crystallographic data. Proteins-Structure Function and Genetics, 31(2), 116 - 127.
Groenhof, G., Lensink, M. F., & Berendsen, H. J. C. (1998). Exploring the photoactive yellow protein photocycle by combining quantum mechanics and molecular dynamics. Journal of Molecular Graphics & Modelling, 16(4-6), 277 - 277.
Lensink, M. F., Mavri, J., & Berendsen, H. J. C. (1998). Simulation of a slow reaction with quantum character-neutral hydrolysis of a carboxylic ester. Journal of Molecular Graphics & Modelling, 16(4-6), 278 - 278.
Langedijk, J. P. M., de Groot, B. L., Berendsen, H. J. C., & van Oirschot, J. T. (1998). Structural homology of the central conserved region of the attachment protein G of respiratory syncytial virus with the fourth subdomain of 55-kDa tumor necrosis factor receptor. Virology, 243(2), 293 - 302.
Roccatano, D., Berendsen, H. J. C., D'Angelo, P., & d' Angelo, P. (1998). Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended x-ray absorption fine structure spectroscopy: A case study of Sr2+ in methanol solution: A case study of Sr2+ in methanol solution. Journal of Chemical Physics, 108(22), 9487 - 9497.
Roccatano, D., Amadei, A., Apol, M. E. F., Di Nola, A., Berendsen, H. J. C., & Di Nora, A. (1998). Application of the quasi-Gaussian entropy theory to molecular dynamics simulations of Lennard-Jones fluids. Journal of Chemical Physics, 109(15), 6358 - 6363.
Sansom, M. S. P., Breed, J., Berendsen, H. J. C., & Tieleman, P. (1998). Alamethicin channels - Simulation studies. Biophysical Journal, 74(2), A232 - A232.
Sansom, M. S. P., Tieleman, D. P., Forrest, L. R., & Berendsen, H. J. C. (1998). Molecular dynamics simulations of membranes with embedded proteins and peptides: porin, alamethicin and influenza virus M2: porin, alamethicin and influenza virus M2. Biochemical Society Transactions, 26(3), 438 - 443.
Tieleman, D. P., & Berendsen, H. J. C. (1998). A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophysical Journal, 74(6), 2786 - 2801.
Tieleman, D. P., & Berendsen, H. J. C. (1998). A molecular dynamics study of the pores formed by E-coli OmpF porin in a fully hydrated pope bilayer. Biophysical Journal, 74(2), A392 - A392.
Tieleman, D. P., Breed, J., Berendsen, H. J. C., & Sansom, M. S. P. (1998). Alamethicin channels in a membrane: molecular dynamics simulations: molecular dynamics simulations. Faraday Discussions, 111(111), 209 - 223.
van der Spoel, D., van Maaren, P. J., & Berendsen, H. J. C. (1998). A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field: Derivation of water models optimized for use with a reaction field. Journal of Chemical Physics, 108(24), 10220 - 10230.
Vriend, G., Berendsen, H. J. C., van den Burg, B., Venema, G., & Eijsink, V. G. H. (1998). Early steps in the unfolding of thermolysin-like proteases. The Journal of Biological Chemistry, 273(52), 35074 - 35077.
Veltman, O. R., Berendsen, H. J. C., & Venema, G. (1998). A single calcium binding site is crucial for the calcium dependent thermal stability of thermolys in-like proteases. Biochemistry, 37, 5312 - 5319.
Feenstra, K. A., & Berendsen, H. J. C. (1998). The domain decomposition of a single-domain protein. In P. Grassberger, G. T. Barkema, & W. Nadler (Eds.), WORKSHOP ON MONTE CARLO APPROACH TO BIOPOLYMERS AND PROTEIN FOLDING (pp. 255-267). SINGAPORE: World Scientific Publishing.
Liebrand, W. B. G., Berendsen, H. J. C., Petkov, N., Wansbeek, T. J., Nerbonne, J., Zwierstra, R. P., ... Duim, L. A. V. D. (1998). ICT-strategie RuG: de bijdrage van informatie- en communicatietechnologie aan onderwijs en onderzoek. Groningen: s.n.

1997

Tieleman, D. P., Marrink, S. J., & Berendsen, H. J. C. (1997). A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochimica et Biophysica Acta-Reviews on Biomembranes, 1331(3), 235-270. DOI: 10.1016/S0304-4157(97)00008-7
van Aalten, D. M. F., Conn, D. A., de Groot, B. L., Berendsen, H. J. C., Findlay, J. B. C., & Amadei, A. (1997). Protein dynamics derived from clusters of crystal structures. Biophysical Journal, 73(6), 2891-2896.
de Groot, B. L., van Aalten, D. M. F., Scheek, R. M., Amadei, A., Vriend, G., & Berendsen, H. J. C. (1997). Prediction of protein conformational freedom from distance constraints. Proteins-Structure Function and Genetics, 29(2), 240-251.
Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463-1472.
van der Spoel, D., & Berendsen, H. J. C. (1997). Molecular dynamics simulations of leu-enkephalin in water and DMSO. Biophysical Journal, 72(5), 2032-2041.
Hayward, S., Kitao, A., & Berendsen, H. J. C. (1997). Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins-Structure Function and Genetics, 27(3), 425-437.
Amadei, A., Apol, M. E. F., & Berendsen, H. J. C. (1997). Extensions of the quasi-Gaussian entropy theory. Journal of Chemical Physics, 106(5), 1893-1912.
van Aalten, D. M. F., de Groot, B. L., Findlay, J. B. C., Berendsen, H. J. C., & Amadei, A. (1997). A comparison of techniques for calculating protein essential dynamics. Journal of Computational Chemistry, 18(2), 169-181.
deVries, A. H., vanDuijnen, P. T., Zijlstra, R. W. J., & Swart, M. (1997). Thole's interacting polarizability model in computational chemistry practice. Journal of Electron Spectroscopy and Related Phenomena, 86(1-3), 49-55.

1996

Marrink, S. J., & Berendsen, H. J. C. (1996). Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations. Journal of Physical Chemistry, 100(41), 16729 - 16738. DOI: 10.1021/jp952956f
Marrink, S. J., Jähnig, F., & Berendsen, H. J. C. (1996). Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophysical Journal, 71(2), 632 - 647. DOI: 10.1016/S0006-3495(96)79264-0
Marrink, S. J., Sok, R. M., & Berendsen, H. J. C. (1996). Free volume properties of a simulated lipid membrane. Journal of Chemical Physics, 104(22), 9090 - 9099. DOI: 10.1063/1.471442
López Cascales, J. J., García de la Torre, J., Marrink, S. J., & Berendsen, H. J. C. (1996). Molecular dynamics simulation of a charged biological membrane. Journal of Chemical Physics, 104(7), 2713 - 2720. DOI: 10.1063/1.470992
Marrink, S. J., Tieleman, D. P., Buuren , van, A. R., & Berendsen, H. J. C. (1996). Membranes and water: An interesting relationship. Faraday Discussions, 103(3), 191-201. DOI: 10.1039/fd9960300191
van der Spoel, D., Feenstra, K. A., Hemminga, M. A., & Berendsen, H. J. C. (1996). Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic mottle virus coat protein in solution with phosphate ions. Biophysical Journal, 71(6), 2920 - 2932.
de Groot, B. L., Amadei, A., Scheek, R. M., van Nuland, N. A. J., & Berendsen, H. J. C. (1996). An extended sampling of the configurational space of HPr from E-coli. Proteins-Structure Function and Genetics, 26(3), 314 - 322.
Amadei, A., Roccatano, D., Apol, M. E. F., Berendsen, H. J. C., & Di Nola, A. (1996). Prediction of the liquid-vapor equilibrium pressure using the quasi-Gaussian entropy theory. Journal of Chemical Physics, 105(16), 7022 - 7025.
vanAalten, D. M. F., deGroot, B. L., Berendsen, H. J. C., & Findlay, J. B. C. (1996). Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins. Biochemical Journal, 319, 543-550.
de Groot, B. L., van Aalten, D. M. F., Amadei, A., & Berendsen, H. J. C. (1996). The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophysical Journal, 71(4), 1707-1713.
Lijnzaad, P., Berendsen, H. J. C., & Argos, P. (1996). A method for detecting hydrophobic patches protein. Proteins-Structure Function and Genetics, 26(2), 192 - 203.
vanderSpoel, D., vanBuuren, A. R., Tieleman, D. P., & Berendsen, H. J. C. (1996). Molecular dynamics simulations of peptides from BPTI: A closer look at amide-aromatic interactions. Journal of Biomolecular Nmr, 8(3), 229-238. DOI: 10.1007/bf00410322
Van der Spoel, D., De Groot, B. L., Hayward, S., Berendsen, H. J. C., & Vogel, H. J. (1996). Bending of the calmodulin central helix: A theoretical study. Protein Science, 5(10), 2044-2053.
Tieleman, D. P., & Berendsen, H. J. C. (1996). Molecular dynamics simulations of a fully hydrated dipalmitoyl phosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. Journal of Chemical Physics, 105(11), 4871 - 4880.
Lensink, M. F., Mavri, J., & Berendsen, H. J. C. (1996). Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integrator. Journal of Computational Chemistry, 17(11), 1287-1295. DOI: 10.1002/(sici)1096-987x(199608)17:11<1287::aid-jcc1>3.3.co;2-s
Lijnzaad, P., Berendsen, H. J. C., & Argos, P. (1996). Hydrophobic patches on the surfaces of protein structures. Proteins-Structure Function and Genetics, 25(3), 389 - 397.
Apol, M. E. F., Amadei, A., & Berendsen, H. J. C. (1996). Derivation of a thermodynamic closure relation in the isothermal-isobaric ensemble using quasi-Gaussian entropy theory. Chemical Physics Letters, 256(1-2), 172 - 178.
Cascales, J. J. L., Berendsen, H. J. C., & delaTorre, J. G. (1996). Molecular dynamics simulation of water between two charged layers of dipalmitoylphosphatidylserine. Journal of Physical Chemistry, 100(21), 8621 - 8627.
vanBuuren, A. R., Tieleman, D. P., deVlieg, J., & Berendsen, H. J. C. (1996). Cosurfactants lower surface tension of the diglyceride/water interface: A molecular dynamics study. Langmuir, 12(10), 2570-2579.
Apol, M. E. F., Amadei, A., & Berendsen, H. J. C. (1996). Application of the quasi-Gaussian entropy theory to the calculation of thermodynamic properties of water and methane in the liquid and gas phase. Journal of Chemical Physics, 104(17), 6665 - 6678.
de Groot, B. L., Amadei, A., van Aalten, D. M. F., & Berendsen, H. J. C. (1996). Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. Journal of Biomolecular Structure & Dynamics, 13(5), 741 - 751.
van der Spoel, D., Vogel, H. J., & Berendsen, H. J. C. (1996). Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein. Proteins-Structure Function and Genetics, 24(4), 450 - 466.
Berendsen, H. J. C., & Mavri, J. (1996). Approach to nonadiabatic transitions by density matrix evolution and molecular dynamics simulations. International Journal of Quantum Chemistry, 57(5), 975 - 983.
Berendsen, H. J. C. (1996). Bio-molecular dynamics comes of age. Science, 271(5251), 954 - 955.
Amadei, A., Linssen, A. B. M., de Groot, B. L., van Aalten, D. M. F., & Berendsen, H. J. C. (1996). An efficient method for sampling the essential subspace of proteins. Journal of Biomolecular Structure & Dynamics, 13(4), 615-625.
van Aalten, D. M. F., Amadei, A., Bywater, R., Findlay, J. B. C., Berendsen, H. J. C., Sander, C., & Stouten, P. F. W. (1996). Comparison of structural and dynamic properties of different simulation methods applied to SH3. Biophysical Journal, 70(2), 684 - 692.
Amadei, A., Apol, M. E. F., DiNola, A., & Berendsen, H. J. C. (1996). The quasi-Gaussian entropy theory: Free energy calculations based on the potential energy distribution function. Journal of Chemical Physics, 104(4), 1560-1574.
Amadei, A., Apol, M. E. F., Di Nola, A., & Berendsen, H. J. C. (1996). The quasi-Gaussian entropy theory: Free energy calculations based on the potential energy distribution function. Journal of Chemical Physics, 104(4), 1560 - 1574.
Tieleman, D. P., Lopez, C. J. J., & Berendsen, H. J. C. (1996). Molecular dynamics studies of lipids and proteins of the E-coli outer membrane: POPE and OmpF. Progress in Biophysics & Molecular Biology, 65, PC443-PC443.
van Buuren, A. R., Tieleman, D. P., de Vlieg, J., & Berendsen, H. J. C. (1996). Cosurfactants lower surface tension of the diglyceride/water interface: A molecular dynamics study. Langmuir, 12(10), 2570 - 2579. DOI: 10.1021/la960113p
Borstnik, . N. V., Robinson, G. W., Haymet, A. D. J., Paulaitis, M. E., Luzar, A., Hummer, G., ... Penfold, R. (1996). General discussion. Faraday Discussions, 103, 91-116.
Duijnen , van, P. T., & de Vries, A. H. (1996). Direct reaction field force field: A consistent way to connect and combine quantum-chemical and classical descriptions of molecules. International Journal of Quantum Chemistry, 60(6), 1111-1132.
Zijlstra, R. W. J., van Duijnen, P. T., & de Vries, A. (1996). Polarization of the excited states of twisted ethylene in a non-symmetrical environment. Chemical Physics, 204(2-3), 439-446.
Devries, A. H., & VanDuijnen, P. T. (1996). Solvatochromism of the pi*. International Journal of Quantum Chemistry, 57(6), 1067 - 1076. DOI: 10.1002/(sici)1097-461x(1996)57:6<1067::aid-qua5>3.0.co;2-r

1995

Buuren, A. R. V., Marrink, S-J., & Berendsen, H. J. C. (1995). Characterisation of aqueous interfaces with different hydrophobicities by molecular dynamics. Colloids and Surfaces A-Physicochemical and Engineering Aspects, 102(41). DOI: 10.1016/0927-7757(95)03227-5
van Aalten, D. M. F., Findlay, J. B. C., Amadei, A., & Berendsen, H. J. C. (1995). Essential dynamics of the cellular retinol-binding protein - Evidence for ligand-induced conformational changes. Protein Engineering, 8(11), 1129-1135.
Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS - A MESSAGE-PASSING PARALLEL MOLECULAR-DYNAMICS IMPLEMENTATION. Computer Physics Communications, 91(1-3), 43-56. DOI: 10.1016/0010-4655(95)00042-e
MAVRI, J., & BERENDSEN, H. J. C. (1995). CALCULATION OF THE PROTON-TRANSFER RATE USING DENSITY-MATRIX EVOLUTION AND MOLECULAR-DYNAMICS SIMULATIONS - INCLUSION OF THE PROTON EXCITED-STATES. Journal of Physical Chemistry, 99(34), 12711-12717.
JORDAN, P. C., VAN MAAREN, P. J., MAVRI, J., VAN DER SPOEL, D., & BERENDSEN, H. J. C. (1995). TOWARDS PHASE TRANSFERABLE POTENTIAL FUNCTIONS - METHODOLOGY AND APPLICATION TO NITROGEN. Journal of Chemical Physics, 103(6), 2272 - 2285.
VANBUUREN, A. R., DEVLIEG, J., & BERENDSEN, H. J. C. (1995). STRUCTURAL-PROPERTIES OF 1,2-DIACYL-SN-GLYCEROL IN BULK AND AT THE WATER INTERFACE BY MOLECULAR-DYNAMICS. Langmuir, 11(8), 2957-2965. DOI: 10.1021/la00008a019
Bekker, H., Berendsen, H. J. C., & Gunsteren, W. F. (1995). FORCE AND VIRIAL OF TORSIONAL-ANGLE-DEPENDENT POTENTIALS. Journal of Computational Chemistry, 16(5), 527-533.
van Aalten, D. M. F., Amadei, A., Linssen, A. B. M., Eijsink, V. G. H., Vriend, G., & Berendsen, H. J. C. (1995). THE ESSENTIAL DYNAMICS OF THERMOLYSIN - CONFIRMATION OF THE HINGE-BENDING MOTION AND COMPARISON OF SIMULATIONS IN VACUUM AND WATER. Proteins-Structure Function and Genetics, 22(1), 45-54.
VANDRUNEN, R., VANDERSPOEL, D., & BERENDSEN, H. J. C. (1995). GROMACS - A SOFTWARE PACKAGE AND A PARALLEL COMPUTER FOR MOLECULAR-DYNAMICS. Abstracts of Papers of the American Chemical Society, 209, 49-COMP.
Bekker, H., Dijkstra, E. J., Renardus, M. K. R., & Berendsen, H. J. C. (1995). AN EFFICIENT, BOX SHAPE INDEPENDENT NONBONDED FORCE AND VIRIAL ALGORITHM FOR MOLECULAR-DYNAMICS. Molecular Simulation, 14(3), 137 - 151. DOI: 10.1080/08927029508022012
Drenth, F. J., Berendsen, H. J. C., & Tissen, J. T. W. M. (1995). Hydrodynamic protein interactions JGEM. The FASEB Journal, 9(6), A1467 - A1467.
AMADEI, A., LINSSEN, A. B. M., DEGROOT, B. L., & BERENDSEN, H. J. C. (1995). Essential degrees of freedom of proteins. In A. Pullman, J. Jortner, & B. Pullman (Eds.), MODELLING OF BIOMOLECULAR STRUCTURES AND MECHANISMS (pp. 85-93). (JERUSALEM SYMPOSIA ON QUANTUM CHEMISTRY AND BIOCHEMISTRY; Vol. 27). DORDRECHT: Kluwer Academic Publishers.
DEVRIES, A. H., VANDUIJNEN, P. T., JUFFER, A. H., RULLMANN, J. A. C., DIJKMAN, J. P., MERENGA, H., & THOLE, B. T. (1995). IMPLEMENTATION OF REACTION FIELD METHODS IN QUANTUM-CHEMISTRY COMPUTER CODES (VOL 16, PG 37, 1995). Journal of Computational Chemistry, 16(11), 1445-1446.
DEVRIES, A. H., VANDUIJNEN, P. T., JUFFER, A. H., RULLMANN, J. A. C., DIJKMAN, J. P., MERENGA, H., & THOLE, B. T. (1995). IMPLEMENTATION OF REACTION FIELD METHODS IN QUANTUM-CHEMISTRY COMPUTER CODES. Journal of Computational Chemistry, 16(1), 37-55. DOI: 10.1002/jcc.540161113
VANDUIJNEN, P. T., & DEVRIES, A. H. (1995). UTOPIA DIELECTRICA. International Journal of Quantum Chemistry, 523-531.
de Vries, A. H. (1995). Modelling condensed-phase systems: from quantum chemistry to molecular models Groningen: s.n.

1994

Marrink, S-J., & Berendsen, H. J. C. (1994). Simulation of Water Transport through a Lipid Membrane. The Journal of Physical Chemistry, 98(15), 4155-4168. DOI: 10.1021/j100066a040
Egberts, E., Marrink, S-J., & Berendsen, H. J. C. (1994). Molecular dynamics simulation of a phospholipid membrane. European biophysics journal with biophysics letters, 22(6), 423-436. DOI: 10.1007/BF00180163
Marrink, S. J. (1994). Permeation of small molecules across lipid membranes. A molecular dynamics study. s.n.
TISSEN, J. T. W. M., DRENTH, J., BERENDSEN, H. J. C., & FRAAIJE, J. G. E. M. (1994). MICROHYDRODYNAMICS SIMULATION OF PROTEIN CRYSTALLIZATION .1. STATIC CALCULATIONS. Biophysical Journal, 67(5), 1801-1805.
MAVRI, J., LENSINK, M., & BERENDSEN, H. J. C. (1994). TREATMENT OF INELASTIC-COLLISIONS OF A PARTICLE WITH A QUANTUM HARMONIC-OSCILLATOR BY DENSITY-MATRIX EVOLUTION. Molecular Physics, 82(6), 1249-1257.
TISSEN, J. T. W. M., FRAAIJE, J. G. E. M., DRENTH, J., & BERENDSEN, H. J. C. (1994). MESOSCOPIC THEORIES FOR PROTEIN CRYSTAL-GROWTH. Acta Crystallographica Section D: Biological Crystallography, 50, 569-571.
DINOLA, A., ROCCATANO, D., & BERENDSEN, H. J. C. (1994). MOLECULAR-DYNAMICS SIMULATION OF THE DOCKING OF SUBSTRATES TO PROTEINS. Proteins-Structure Function and Bioinformatics, 19(3), 174-182.
MAVRI, J., & BERENDSEN, H. J. C. (1994). DYNAMICAL SIMULATION OF A QUANTUM HARMONIC-OSCILLATOR IN A NOBLE-GAS BATH BY DENSITY-MATRIX EVOLUTION. Physical Review E, 50(1), 198-204.
MAVRI, J., & BERENDSEN, H. J. C. (1994). TREATMENT OF NONADIABATIC TRANSITIONS BY DENSITY-MATRIX EVOLUTION AND MOLECULAR-DYNAMICS SIMULATIONS. Journal of Molecular Structure, 322, 1-7.
VANBUUREN, A. R., & BERENDSEN, H. J. C. (1994). MOLECULAR-DYNAMICS SIMULATIONS OF CARBOHYDRATE-BASED SURFACTANTS IN SURFACTANT WATER OIL SYSTEMS. Langmuir, 10(6), 1703-1713.
van Nuland, N., Hangyi, I. W., Schaik, R. C. V., Berendsen, H. J. C., Gunsteren, W. F. V., Scheek, R. M., & Robillard, G. T. (1994). The High-resolution Structure of the Histidine-containing Phosphocarrier Protein HPr from Escherichia coli Determined by Restrained Molecular Dynamics from Nuclear Magnetic Resonance Nuclear Overhauser Effect Data. Journal of Molecular Biology, 237(5), 544-559. DOI: 10.1006/jmbi.1994.1254
LEENDERS, R., VANGUNSTEREN, W. F., BERENDSEN, H. J. C., & VISSER, A. J. W. G. (1994). MOLECULAR-DYNAMICS SIMULATIONS OF OXIDIZED AND REDUCED CLOSTRIDIUM-BEIJERINCKII FLAVODOXIN. Biophysical Journal, 66(3), 634-645.
YONEYA, M., & BERENDSEN, H. J. C. (1994). MOLECULAR-DYNAMICS SIMULATIONS OF CHIRAL NEMATIC LIQUID-CRYSTALS. Journal of the Physical Society of Japan, 63(3), 1025-1030.
YONEYA, M., BERENDSEN, H. J. C., & HIRASAWA, K. (1994). A NONITERATIVE MATRIX-METHOD FOR CONSTRAINT MOLECULAR-DYNAMICS SIMULATIONS. Molecular Simulation, 13(6), 395-405.

1993

BERENDSEN, H. J. C., & MARRINK, S. J. (1993). Molecular-dynamics of water transport through membranes - water from solvent to solute. Pure and Applied Chemistry, 65(12), 2513-2520. DOI: 10.1351/pac199365122513
Marrink, S-J., Berkowitz, M., & Berendsen, H. J. C. (1993). Molecular Dynamics Simulation of a Membrane/Water Interface: The Ordering of Water and Its Relation to the Hydration Force. Langmuir, 9(11). DOI: 10.1021/la00035a062
Buuren, A. R. V., Marrink, S-J., & Berendsen, H. J. C. (1993). A Molecular Dynamics Study of the Decane/Water Interface. The Journal of Physical Chemistry, 97(36). DOI: 10.1021/j100138a023
BERENDSEN, H. J. C., & MAVRI, J. (1993). QUANTUM SIMULATION OF REACTION DYNAMICS BY DENSITY-MATRIX EVOLUTION. Journal of Physical Chemistry, 97(51), 13464-13468.
MAVRI, J., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1993). INFLUENCE OF SOLVENT ON INTRAMOLECULAR PROTON-TRANSFER IN HYDROGEN MALONATE - MOLECULAR-DYNAMICS SIMULATION STUDY OF TUNNELING BY DENSITY-MATRIX EVOLUTION AND NONEQUILIBRIUM SOLVATION. Journal of Physical Chemistry, 97(51), 13469-13476.
AHLSTROM, P., & BERENDSEN, H. J. C. (1993). A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS. Journal of Physical Chemistry, 97(51), 13691-13702.
VANSCHAIK, R. C., BERENDSEN, H. J. C., TORDA, A. E., & VANGUNSTEREN, W. F. (1993). A STRUCTURE REFINEMENT METHOD BASED ON MOLECULAR-DYNAMICS IN 4 SPATIAL DIMENSIONS. Journal of Molecular Biology, 234(3), 751-762.
AMADEI, A., LINSSEN, A. B. M., & BERENDSEN, H. J. C. (1993). ESSENTIAL DYNAMICS OF PROTEINS. Proteins-Structure Function and Bioinformatics, 17(4), 412-425.
VANBUUREN, A. R., & BERENDSEN, H. J. C. (1993). MOLECULAR-DYNAMICS SIMULATION OF THE STABILITY OF A 22-RESIDUE ALPHA-HELIX IN WATER AND 30-PERCENT TRIFLUOROETHANOL. Biopolymers, 33(8), 1159-1166.
JUFFER, A. H., & BERENDSEN, H. J. C. (1993). DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS. Molecular Physics, 79(3), 623-644.
HEINER, A. P., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1993). STRUCTURE PREDICTION OF SUBTILISIN BPN' MUTANTS USING MOLECULAR-DYNAMICS METHODS. Protein Engineering, 6(4), 397-408.
YUNYU, S., MARK, A. E., WANG, C. X., HUANG, F. H., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1993). CAN THE STABILITY OF PROTEIN MUTANTS BE PREDICTED BY FREE-ENERGY CALCULATIONS. Protein Engineering, 6(3), 289-295.
JONES, S. T., AHLSTROM, P., BERENDSEN, H. J. C., & PICKERSGILL, R. W. (1993). MOLECULAR-DYNAMICS SIMULATION OF A PHOSPHOLIPASE-A2 SUBSTRATE COMPLEX. Biochimica et biophysica acta, 1162(1-2), 135-142.
BEKKER, H., DIJKSTRA, E. J., & BERENDSEN, H. J. C. (1993). MOLECULAR-DYNAMICS SIMULATION ON AN I860 BASED RING ARCHITECTURE. Supercomputer, 10(2), 4-10.
BEKKER, H., BERENDSEN, H. J. C., DIJKSTRA, E. J., ACHTEROP, S., VONDRUMEN, R., VANDERSPOEL, D., ... RENARDUS, M. K. R. (1993). GROMACS - A PARALLEL COMPUTER FOR MOLECULAR-DYNAMICS SIMULATIONS. In R. A. DeGroot, & J. Nadrchal (Eds.), PHYSICS COMPUTING '92 (pp. 252-256). SINGAPORE: World Scientific Publishing.
BEKKER, H., BERENDSEN, H. J. C., DIJKSTRA, E. J., ACHTEROP, S., VONDRUMEN, R., SIJBERS, A., ... VANDERSPOEL, D. (1993). GROMACS METHOD OF VIRIAL CALCULATION USING A SINGLE SUM. In R. A. DeGroot, & J. Nadrchal (Eds.), PHYSICS COMPUTING '92 (pp. 257-261). SINGAPORE: World Scientific Publishing.
DEVRIES, A. H., VANDUIJNEN, P. T., & JUFFER, A. H. (1993). SUCCESS AND PITFALLS OF THE DIELECTRIC CONTINUUM MODEL IN QUANTUM-CHEMICAL CALCULATIONS. International Journal of Quantum Chemistry, 451-466.

1992

Berendsen, H., Egberts, B., Marrink, S., & Ahlstroem, P. (1992). Molecular Dynamics Simulations of Phospholipid Membranes and Their Interaction with Phospholipase A2. In A. Pullman, J. Jortner, & B. Pullman (Eds.), Membrane Proteins: Structures, Interactions and Models (1 ed., Vol. 1, pp. 457-470). ( The Jerusalem Symposia on Quantum Chemistry and Biochemistry; Vol. 25). Springer International Publishing. DOI: 10.1007/978-94-011-2718-9_37
HEINER, A. P., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1992). MD SIMULATION OF SUBTILISIN BPN' IN A CRYSTAL ENVIRONMENT. Proteins-Structure Function and Bioinformatics, 14(4), 451-464.
SOK, R. M., & BERENDSEN, H. J. C. (1992). MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE. Abstracts of Papers of the American Chemical Society, 203, 619-POLY.
VANSCHAIK, R. C., VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1992). CONFORMATIONAL SEARCH BY POTENTIAL-ENERGY ANNEALING - ALGORITHM AND APPLICATION TO CYCLOSPORINE-A. Journal of Computer-Aided Molecular Design, 6(2), 97-112.
SOK, R. M., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1992). MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE. Journal of Chemical Physics, 96(6), 4699-4704.
DEVRIES, A. H., & VANDUIJNEN, P. T. (1992). THEORETICAL CALCULATION OF TAUTOMER EQUILIBRIA OF 4-SUBSTITUTED IMIDAZOLES IN THE GAS-PHASE AND IN SOLUTION. Biophysical Chemistry, 43(2), 139-147.

1991

VRIEND, G., BERENDSEN, H. J. C., VANDERZEE, . N. V., VANDENBURG, B., VENEMA, G., & EIJSINK, V. G. H. (1991). STABILIZATION OF THE NEUTRAL PROTEASE OF BACILLUS-STEAROTHERMOPHILUS BY REMOVAL OF A BURIED WATER MOLECULE. Protein Engineering, 4(8), 941-945.
MARK, A. E., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1991). CONFORMATIONAL FLEXIBILITY OF AQUEOUS MONOMERIC AND DIMERIC INSULIN - A MOLECULAR-DYNAMICS STUDY. Biochemistry, 30(45), 10866-10872.
JUFFER, A. H., BOTTA, E. F. F., VANKEULEN, B. A. M., VANDERPLOEG, A., & BERENDSEN, H. J. C. (1991). THE ELECTRIC-POTENTIAL OF A MACROMOLECULE IN A SOLVENT - A FUNDAMENTAL APPROACH. Journal of computational physics, 97(1), 144-171.
EIJSINK, V. G. H., VANDENBURG, B., VRIEND, G., BERENDSEN, H. J. C., & VENEMA, G. (1991). THERMOSTABILITY OF BACILLUS-SUBTILIS NEUTRAL PROTEASE. Biochemistry international, 24(3), 517-525.
MARK, A. E., VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1991). CALCULATION OF RELATIVE FREE-ENERGY VIA INDIRECT PATHWAYS. Journal of Chemical Physics, 94(5), 3808-3816.
TINGE, J. T., TENDE, H. C. O., BERENDSEN, H. J. C., & DRINKENBURG, A. A. H. (1991). THE ABSORPTION OF PROPANE AND ETHENE IN SLURRIES OF ACTIVATED CARBON IN WATER .2. Chemical Engineering Science, 46(1), 343-350.
VANGUNSTEREN, W. F., GROS, P., TORDA, A. E., BERENDSEN, H. J. C., & VANSCHAIK, R. C. (1991). ON DERIVING SPATIAL PROTEIN-STRUCTURE FROM NMR OR X-RAY-DIFFRACTION DATA. Ciba foundation symposia, 161, 150-166.

1990

VANMIERLO, C. P. M., LIJNZAAD, P., MULLER, F., BERENDSEN, H. J. C., & DEVLIEG, J. (1990). TERTIARY STRUCTURE OF 2-ELECTRON REDUCED MEGASPHAERA-ELSDENII FLAVODOXIN AND SOME IMPLICATIONS, AS DETERMINED BY 2-DIMENSIONAL H-1-NMR AND RESTRAINED MOLECULAR-DYNAMICS. European Journal of Biochemistry, 194(1), 185-198.
VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1990). COMPUTER-SIMULATION OF MOLECULAR-DYNAMICS - METHODOLOGY, APPLICATIONS, AND PERSPECTIVES IN CHEMISTRY. Angewandte Chemie-International Edition in English, 29(9), 992-1023.

1989

MAKINEN, M. W., TROYER, J. M., VANDERWERFF, H., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1989). DYNAMICAL STRUCTURE OF CARBOXYPEPTIDASE-A. Journal of Molecular Biology, 207(1), 201-216.
KAMMAN, R. L., STOMP, G. P., & BERENDSEN, H. J. C. (1989). UNIFIED MULTIPLE-FEATURE COLOR DISPLAY FOR MR IMAGES. Magnetic resonance in medicine, 9(2), 240-253.
DEVLIEG, J., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1989). AN NMR-BASED MOLECULAR-DYNAMICS SIMULATION OF THE INTERACTION OF THE LAC REPRESSOR HEADPIECE AND ITS OPERATOR IN AQUEOUS-SOLUTION. Proteins-Structure Function and Bioinformatics, 6(2), 104-127.

1988

STRAATSMA, T. P., & BERENDSEN, H. J. C. (1988). FREE-ENERGY OF IONIC HYDRATION - ANALYSIS OF A THERMODYNAMIC INTEGRATION TECHNIQUE TO EVALUATE FREE-ENERGY DIFFERENCES BY MOLECULAR-DYNAMICS SIMULATIONS. Journal of Chemical Physics, 89(9), 5876-5886.
BERENDSEN, H. J. C. (1988). DYNAMIC SIMULATION AS AN ESSENTIAL TOOL IN MOLECULAR MODELING. Journal of Computer-Aided Molecular Design, 2(3), 217-221.
BERENDSEN, H. J. C. (1988). MOLECULAR-DYNAMICS SIMULATION OF A SMECTIC LIQUID-CRYSTAL WITH ATOMIC DETAIL. Journal of Chemical Physics, 89(6), 3718-3732.
KESSLER, H., GRIESINGER, C., LAUTZ, J., MULLER, A., VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1988). CONFORMATIONAL DYNAMICS DETECTED BY NUCLEAR MAGNETIC-RESONANCE NOE VALUES AND J-COUPLING CONSTANTS. Journal of the American Chemical Society, 110(11), 3393-3396.
KAMMAN, R. L., GO, K. G., BROUWER, W., & BERENDSEN, H. J. C. (1988). NUCLEAR MAGNETIC-RESONANCE RELAXATION IN EXPERIMENTAL BRAIN EDEMA - EFFECTS OF WATER CONCENTRATION, PROTEIN-CONCENTRATION, AND TEMPERATURE. Magnetic resonance in medicine, 6(3), 265-274.
Van Gunsteren, W. F., & Berendsen, H. J. C. (1988). A LEAP-FROG ALGORITHM FOR STOCHASTIC DYNAMICS. Molecular Simulation, 1(3), 173-185. DOI: 10.1080/08927028808080941
DEVLIEG, J., SCHEEK, R. M., VANGUNSTEREN, W. F., BERENDSEN, H. J. C., KAPTEIN, R., & THOMASON, J. (1988). COMBINED PROCEDURE OF DISTANCE GEOMETRY AND RESTRAINED MOLECULAR-DYNAMICS TECHNIQUES FOR PROTEIN-STRUCTURE DETERMINATION FROM NUCLEAR MAGNETIC-RESONANCE DATA - APPLICATION TO THE DNA-BINDING DOMAIN OF LAC REPRESSOR FROM ESCHERICHIA-COLI. Proteins-Structure Function and Bioinformatics, 3(4), 209-218.

1987

BERENDSEN, H. J. C., GRIGERA, . N. V., & STRAATSMA, T. P. (1987). THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS. Journal of Physical Chemistry, 91(24), 6269-6271.
BERENDSEN, H. J. C. (1987). BIOPHYSICAL APPLICATIONS OF MOLECULAR-DYNAMICS. Computer Physics Communications, 44(3), 233-242.
KAMMAN, R. L., GO, K. G., VENCKEN, L. M., & BERENDSEN, H. J. C. (1987). INTERPRETATION OF MAGNETIC-RESONANCE IMAGES MAKING USE OF INVITRO EXAMINATIONS OF SPINAL TISSUE. SPINE, 12(3), 257-263.
Kamman, R., Bakker, C. J. G., van Dijk, P., Stomp, G. P., Heiner, A. P., & Berendsen, H. (1987). Multi-exponential relaxation analysis with MR imaging and NMR spectroscopy using fat-water systems. Magnetic Resonance Imaging, 5(5), 381-392.
BERENDSEN, H. J. C., VANGUNSTEREN, W. F., & DEVLIEG, J. (1987). DYNAMIC SIMULATION OF COMPLEX MOLECULAR-SYSTEMS. Acs symposium series, 353, 106-122.

1986

STRAATSMA, T. P., BERENDSEN, H. J. C., & POSTMA, J. P. M. (1986). FREE-ENERGY OF HYDROPHOBIC HYDRATION - A MOLECULAR-DYNAMICS STUDY OF NOBLE-GASES IN WATER. Journal of Chemical Physics, 85(11), 6720-6727.
MAKINEN, M. W., TROYER, J. M., VANDERWERFF, H., BERENDSEN, H. J. C., & VANGUNSTEREN, W. F. (1986). DYNAMIC MOTION IN CARBOXYPEPTIDASE-A. Federation proceedings, 45(6), 1873-1873.
STRAATSMA, T. P., BERENDSEN, H. J. C., & STAM, A. J. (1986). ESTIMATION OF STATISTICAL ERRORS IN MOLECULAR SIMULATION CALCULATIONS. Molecular Physics, 57(1), 89-95.

1985

BERENDSEN, H. J. C. (1985). MOLECULAR-DYNAMICS SIMULATION OF A HYDRATED LIPID BILAYER. Abstracts of Papers of the American Chemical Society, 190(SEP), 10-COL.

1984

REMERIE, K., VANGUNSTEREN, W. F., POSTMA, J. P. M., BERENDSEN, H. J. C., & ENGBERTS, J. B. F. N. (1984). MOLECULAR-DYNAMICS COMPUTER-SIMULATION OF THE HYDRATION OF 2 SIMPLE ORGANIC SOLUTES - COMPARISON WITH THE SIMULATION OF AN EMPTY CAVITY. Molecular Physics, 53(6), 1517-1526.
POSTMA, J. P. M., BERENDSEN, H. J. C., & STRAATSMA, T. P. (1984). INTRAMOLECULAR VIBRATIONS FROM MOLECULAR-DYNAMICS SIMULATIONS OF LIQUID WATER. Journal de physique, 45(NC-7), 31-40.
EDHOLM, O., & BERENDSEN, H. J. C. (1984). ENTROPY ESTIMATION FROM SIMULATIONS OF NON-DIFFUSIVE SYSTEMS. Molecular Physics, 51(4), 1011-1028.
VANGUNSTEREN, W. F., BERENDSEN, H. J. C., COLONNA, F., PERAHIA, D., HOLLENBERG, J. P., & LELLOUCH, D. (1984). ON SEARCHING NEIGHBORS IN COMPUTER-SIMULATIONS OF MACROMOLECULAR SYSTEMS. Journal of Computational Chemistry, 5(3), 272-279.
VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1984). COMPUTER-SIMULATION AS A TOOL FOR TRACING THE CONFORMATIONAL DIFFERENCES BETWEEN PROTEINS IN SOLUTION AND IN THE CRYSTALLINE STATE. Journal of Molecular Biology, 176(4), 559-564.
BERENDSEN, H. J. C., VANGUNSTEREN, W. F., POSTMA, J. P. M., & Hermans, J. (1984). A CONSISTENT EMPIRICAL POTENTIAL FOR WATER-PROTEIN INTERACTIONS. Biopolymers, 23(8), 1513-1518.
DINOLA, A., BERENDSEN, H. J. C., & EDHOLM, O. (1984). FREE-ENERGY DETERMINATION OF POLYPEPTIDE CONFORMATIONS GENERATED BY MOLECULAR-DYNAMICS. Macromolecules, 17(10), 2044-2050.
BERENDSEN, H. J. C., POSTMA, J. P. M., VANGUNSTEREN, W. F., DINOLA, A., & HAAK, . N. V. (1984). MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH. Journal of Chemical Physics, 81(8), 3684-3690.

1983

Go, K., van Dijk, P., Luiten, A. L., Brouwer-van Herwijnen, A. A., van der Leeuw, I. C. L., Kamman, R., ... Berendsen, H. (1983). Interpretation of nuclear magnetic resonance tomograms of the brain. Journal of Neurosurgery, 59(4), 574-584.
Edholm, O., Berendsen, H., & van der Ploeg, P. (1983). CONFORMATIONAL ENTROPY OF A BILAYER-MEMBRANE DERIVED FROM A MOLECULAR-DYNAMICS SIMULATION. Molecular Physics, 48(2), 379-388.
van der Ploeg, P., & Berendsen, H. (1983). MOLECULAR-DYNAMICS OF A BILAYER-MEMBRANE. Molecular Physics, 49(1), 233-248.
VANGUNSTEREN, W. F., BERENDSEN, H. J. C., HOL, W. G. J., POSTMA, J. P. M., & Hermans, J. (1983). COMPUTER-SIMULATION OF THE DYNAMICS OF HYDRATED PROTEIN CRYSTALS AND ITS COMPARISON WITH X-RAY DATA. Proceedings of the national academy of sciences of the united states of america-Biological sciences, 80(14), 4315-4319.

1982

van der Ploeg, P., & Berendsen, H. (1982). MOLECULAR-DYNAMICS SIMULATION OF A BILAYER-MEMBRANE. Journal of Chemical Physics, 76(6), 3271-3276.
POST, J. F. M., JAMES, E., & BERENDSEN, H. J. C. (1982). MULTIPULSE FLUORINE NMR EXPERIMENTS ON LYOTROPIC LIQUID-CRYSTALS .1. DETERMINATION OF ORDER PARAMETER TENSOR. Journal of Magnetic Resonance, 47(2), 251-263.
POST, J. F. M., KAMMAN, R. L., & BERENDSEN, H. J. C. (1982). MULTIPULSE FLUORINE NMR EXPERIMENTS ON LYOTROPIC LIQUID-CRYSTALS .2. PHASE-TRANSITIONS IN POTASSIUM 4,4-DIFLUOROMYRISTATE D2O. Journal of Magnetic Resonance, 47(2), 264-281.
VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1982). ALGORITHMS FOR BROWNIAN DYNAMICS. Molecular Physics, 45(3), 637-647.
VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1982). MOLECULAR-DYNAMICS - PERSPECTIVE FOR COMPLEX-SYSTEMS. Biochemical Society Transactions, 10(5), 301-305.
VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1982). ON THE FLUCTUATION DISSIPATION THEOREM FOR INTERACTING BROWNIAN PARTICLES. Molecular Physics, 47(3), 721-723.
POSTMA, J. P. M., BERENDSEN, H. J. C., & HAAK, . N. V. (1982). THERMODYNAMICS OF CAVITY FORMATION IN WATER - A MOLECULAR-DYNAMICS STUDY. Faraday symposia of the chemical society, (17), 55-67.

1981

VANGUNSTEREN, W. F., BERENDSEN, H. J. C., & RULLMANN, J. A. C. (1981). STOCHASTIC DYNAMICS FOR MOLECULES WITH CONSTRAINTS BROWNIAN DYNAMICS OF NORMAL-ALKANES. Molecular Physics, 44(1), 69-95.
POST, J. F. M., DERUITER, E. E. J., & BERENDSEN, H. J. C. (1981). A FLUORINE NMR-STUDY OF MODEL MEMBRANES CONTAINING F-19-LABELED PHOSPHOLIPIDS AND AN INTRINSIC MEMBRANE-PROTEIN. FEBS Letters, 132(2), 257-260.

1980

HALLENGA, K., GRIGERA, . N. V., & BERENDSEN, H. J. C. (1980). INFLUENCE OF HYDROPHOBIC SOLUTES ON THE DYNAMIC BEHAVIOR OF WATER. Journal of Physical Chemistry, 84(19), 2381-2390.

1979

GRIGERA, . N. V., & BERENDSEN, H. J. C. (1979). MOLECULAR DETAILS OF COLLAGEN HYDRATION. Biopolymers, 18(1), 47-57.
GRIGERA, . N. V., VERICAT, F., HALLENGA, K., & BERENDSEN, H. J. C. (1979). DIELECTRIC PROPERTIES OF HYDRATED COLLAGEN. Biopolymers, 18(1), 35-45.

1978

HOL, W. G. J., VANDUIJNEN, P. T., & BERENDSEN, H. J. C. (1978). ALPHA-HELIX DIPOLE AND PROPERTIES OF PROTEINS. Nature, 273(5662), 443-446.
VANGUNSTEREN, W. F., BERENDSEN, H. J. C., & RULLMANN, J. A. C. (1978). INCLUSION OF REACTION FIELDS IN MOLECULAR-DYNAMICS - APPLICATION TO LIQUID WATER. Faraday Discussions, 66, 58-70.

1977

van Dijk, G., Berendsen, H., & Gunsteren, W. F. V. (1977). Studentenregistraties, formulering van uitgangspunten. Universiteit en hogeschool, 24(1), 17 - 29.
BIENKIEWICZ, K. J., BERENDSEN, H. J. C., & ANDREE, P. J. (1977). PROPERTIES OF WATER IN NATIVE AND MODIFIED COLLAGEN. Roczniki chemii, 51(1), 149-158.
EDZES, H. T., GINZBURG, M., GINZBURG, B. Z., & BERENDSEN, H. J. C. (1977). PHYSICAL STATE OF ALKALI IONS IN A HALOBACTERIUM - SOME NMR RESULTS. Experientia, 33(6), 732-734.
VANGUNSTEREN, W. F., & BERENDSEN, H. J. C. (1977). ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS. Molecular Physics, 34(5), 1311-1327.

1976

Robillard, G. T., Tarr, C. E., Vosman, F., & Berendsen, H. J. C. (1976). Similarity of the crystal and solution structure of yeast tRNAPhe. Nature, 262(5567). DOI: 10.1038/262363a0
ROBILLARD, G. T., TARR, C. E., VOSMAN, F., & BERENDSEN, H. J. C. (1976). SIMILARITY OF CRYSTAL AND SOLUTION STRUCTURE OF YEAST TRANSFER-RNAPHE. Nature, 262(5567), 363-369.
MATHURDEVRE, R., BERTINCHAMPS, A. J., & BERENDSEN, H. J. C. (1976). EFFECTS OF GAMMA-IRRADIATION ON HYDRATION CHARACTERISTICS OF DNA AND POLYNUCLEOTIDES .1. NMR-STUDY OF FROZEN H2O AND D2O SOLUTIONS. Radiation Research, 68(2), 197-214.
KALK, A., & BERENDSEN, H. J. C. (1976). PROTON MAGNETIC-RELAXATION AND SPIN DIFFUSION IN PROTEINS. Journal of Magnetic Resonance, 24(3), 343-366.

1975

EDZES, H. T., & BERENDSEN, H. J. C. (1975). PHYSICAL STATE OF DIFFUSIBLE IONS IN CELLS. Annual review of biophysics and bioengineering, 4, 265-285.

1974

SCHOOTUITERKAMP, A. J. M., VANDERDEEN, H., BERENDSEN, H. J., & BOAS, J. F. (1974). COMPUTER-SIMULATION OF EPR-SPECTRA OF MONONUCLEAR AND DIPOLAR COUPLED CU(II) IONS IN NITRIC OXIDE-TREATED AND NITRITE-TREATED HEMOCYANINS AND TYROSINASE. Biochimica et biophysica acta, 372(2), 407-425.

1962

Berendsen, H. J. C. (1962). An NMR study of collagen hydration s.n.
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