Publication

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

Wassenaar, T. A., Ingolfsson, H. I., Boeckmann, R. A., Tieleman, D. P. & Marrink, S. J., May-2015, In : Journal of Chemical Theory and Computation. 11, 5, p. 2144-2155 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

APA

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. https://doi.org/10.1021/acs.jctc.5b00209

Author

Wassenaar, Tsjerk A. ; Ingolfsson, Helgi I. ; Boeckmann, Rainer A. ; Tieleman, D. Peter ; Marrink, Siewert J. / Computational Lipidomics with insane : A Versatile Tool for Generating Custom Membranes for Molecular Simulations. In: Journal of Chemical Theory and Computation. 2015 ; Vol. 11, No. 5. pp. 2144-2155.

Harvard

Wassenaar, TA, Ingolfsson, HI, Boeckmann, RA, Tieleman, DP & Marrink, SJ 2015, 'Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations', Journal of Chemical Theory and Computation, vol. 11, no. 5, pp. 2144-2155. https://doi.org/10.1021/acs.jctc.5b00209

Standard

Computational Lipidomics with insane : A Versatile Tool for Generating Custom Membranes for Molecular Simulations. / Wassenaar, Tsjerk A.; Ingolfsson, Helgi I.; Boeckmann, Rainer A.; Tieleman, D. Peter; Marrink, Siewert J.

In: Journal of Chemical Theory and Computation, Vol. 11, No. 5, 05.2015, p. 2144-2155.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Wassenaar TA, Ingolfsson HI, Boeckmann RA, Tieleman DP, Marrink SJ. Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations. Journal of Chemical Theory and Computation. 2015 May;11(5):2144-2155. https://doi.org/10.1021/acs.jctc.5b00209


BibTeX

@article{31c64537221b40debf4fe9d8378c0856,
title = "Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations",
abstract = "For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complementary method for reverse transformation, at http://cgmartini.nl/. This work highlights the key features of insane and presents a survey of properties for a large range of lipids as a start of a computational lipidomics project.",
keywords = "COARSE-GRAINED MODEL, DYNAMICS SIMULATIONS, FORCE-FIELD, BIOMOLECULAR SIMULATIONS, PHOSPHATIDIC-ACID, PROTEINS, BILAYERS, PHOSPHATIDYLCHOLINES, ORGANIZATION, INSERTION",
author = "Wassenaar, {Tsjerk A.} and Ingolfsson, {Helgi I.} and Boeckmann, {Rainer A.} and Tieleman, {D. Peter} and Marrink, {Siewert J.}",
year = "2015",
month = may,
doi = "10.1021/acs.jctc.5b00209",
language = "English",
volume = "11",
pages = "2144--2155",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "AMER CHEMICAL SOC",
number = "5",

}

RIS

TY - JOUR

T1 - Computational Lipidomics with insane

T2 - A Versatile Tool for Generating Custom Membranes for Molecular Simulations

AU - Wassenaar, Tsjerk A.

AU - Ingolfsson, Helgi I.

AU - Boeckmann, Rainer A.

AU - Tieleman, D. Peter

AU - Marrink, Siewert J.

PY - 2015/5

Y1 - 2015/5

N2 - For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complementary method for reverse transformation, at http://cgmartini.nl/. This work highlights the key features of insane and presents a survey of properties for a large range of lipids as a start of a computational lipidomics project.

AB - For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complementary method for reverse transformation, at http://cgmartini.nl/. This work highlights the key features of insane and presents a survey of properties for a large range of lipids as a start of a computational lipidomics project.

KW - COARSE-GRAINED MODEL

KW - DYNAMICS SIMULATIONS

KW - FORCE-FIELD

KW - BIOMOLECULAR SIMULATIONS

KW - PHOSPHATIDIC-ACID

KW - PROTEINS

KW - BILAYERS

KW - PHOSPHATIDYLCHOLINES

KW - ORGANIZATION

KW - INSERTION

U2 - 10.1021/acs.jctc.5b00209

DO - 10.1021/acs.jctc.5b00209

M3 - Article

VL - 11

SP - 2144

EP - 2155

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 5

ER -

ID: 22983202