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Gromacs development


Gromacs, the world famous simulation software suite, originates from our MD group in Groningen. The “GROningen MAChine for Chemical Simuation” package was developed in the 90s, and is currently one of the most used MD software packages around the world. (www.gromacs.org)

Although its main development now takes place in Sweden, we are still actively involved in developing and implementing new methods and algorithms in Gromacs. Currently our work in this area focuses on the development of improved stochastic dynamics (SD) and dissipative particle dynamics (DPD) integrators and thermostats, as well as on advanced algorithms for coarse-grain and multiscale modeling.

[1] N. Goga, M.N. Melo, A.J. Rzepiela, A.H. De Vries, A. Hadar, S.J. Marrink, H.J.C. Berendsen. Benchmark of schemes for multiscale molecular dynamics simulations. JCTC, 11:1389–1398, 2015
[2] E.A.J.F. Peters, N. Goga, H.J.C. Berendsen. Stochastic Dynamics with Correct Sampling for Constrained Systems JCTC, 10:4208-4220, 2014
[3] N. Goga, A.J. Rzepiela, A.H. de Vries, S.J. Marrink, H.J.C. Berendsen. Efficient algorithms for Langevin and DPD dynamics. JCTC, 8:3637-49, 2012.
[4] M. Bulacu, N. Goga, W. Zhao, G. Rossi, L. Monticelli, X. Periole, D.P. Tieleman, S.J. Marrink. Improved angle potentials for coarse-grained molecular dynamics simulations. JCTC, 9:3282–3292, 2013

Improved algorithm for SD and DPD based on impulsive application of friction and noise. Top: Traditional leap-frog scheme. Bottom: Leap-frog scheme with impulsive phase.
Improved algorithm for SD and DPD based on impulsive application of friction and noise. Top: Traditional leap-frog scheme. Bottom: Leap-frog scheme with impulsive phase.
Last modified:25 June 2015 12.35 a.m.