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- David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
- Journal of Computational Chemistry
- 2005

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor… (More)

Articles you may be interested in Dynamics of a two-level system coupled to a bath of spins Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath In molecular dynamics (MD) simulations the need often arises to maintain… (More)

A numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated. The relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration. The method is applied to a molecular dynamics simulation of a liquid… (More)

- Berk Hess, Henk Bekker, Herman J. C. Berendsen, Johannes G. E. M. Fraaije
- Journal of Computational Chemistry
- 1997

In this article we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix… (More)

- D P Tieleman, S J Marrink, H J Berendsen
- Biochimica et biophysica acta
- 1997

- B L de Groot, D M van Aalten, R M Scheek, A Amadei, G Vriend, H J Berendsen
- Proteins
- 1997

A method is presented that generates random protein structures that fulfil a set of upper and lower interatomic distance limits. These limits depend on distances measured in experimental structures and the strength of the interatomic interaction. Structural differences between generated structures are similar to those obtained from experiment and from MD… (More)

- D P Tieleman, H J Berendsen
- Biophysical journal
- 1998

In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square… (More)

1 ESR Electron Spin Resonance NMR Nuclear Magnetic Resonance MD Molecular Dynamics DPPC dipalmitoylphosphatidylcholine DPPS dipalmitoylphosphatidylserine DMPC dimyristoylphosphatidylcholine DLPE dilaureoylphosphatidylethanolamine POPC dalmitoyloleoylphosphatidylcholine NPT constant number of particles, pressure and temperature NVT constant number of… (More)

We compared Molecular Dynamics simulations of a bilayer of 128 fully hydrated phospholipid (DPPC) molecules, using diierent parameters and macroscopic boundary conditions. The same system was studied under constant pressure, constant volume and constant surface tension boundary conditions, with two diierent sets of charges, the single point charge (SPC) and… (More)

- Gerrit Groenhof, Marc F Lensink, Herman J C Berendsen, Jaap G Snijders, Alan E Mark
- Proteins
- 2002

Molecular dynamics simulation techniques together with time-dependent density functional theory calculations have been used to investigate the effect of photon absorption by a 4-hydroxy-cinnamic acid chromophore on the structural properties of the photoactive yellow protein (PYP) from Ectothiorodospira halophila. The calculations suggest that the protein… (More)