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This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range potentials makes it computationally very efficient. Compared to atomistic models a gain of 3-4 orders of magnitude can be achieved. Micrometer length scales or… (More)

- Cesar A. López, Alex H. de Vries, Siewert J. Marrink
- PLoS Computational Biology
- 2011

The depletion of cholesterol from membranes, mediated by β-cyclodextrin (β-CD) is well known and documented, but the molecular details of this process are largely unknown. Using molecular dynamics simulations, we have been able to study the CD mediated extraction of cholesterol from model membranes, in particular from a pure cholesterol monolayer, at atomic… (More)

- Djurre H. De Jong, Lars V. Schäfer, Alex H. de Vries, Siewert J. Marrink, Herman J. C. Berendsen, Helmut Grubmüller
- Journal of Computational Chemistry
- 2011

With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation… (More)

- Andrzej J. Rzepiela, Lars V. Schäfer, Nicolae Goga, H. Jelger Risselada, Alex H. de Vries, Siewert J. Marrink
- Journal of Computational Chemistry
- 2010

We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via… (More)

- Alex H. de Vries, Paul Sherwood, Simon Collins, Anthony M. Rigby, Marcello S Rigutto, Gert Jan Kramer
- 1999

Proton-energy differences, ammonia adsorption, and D/H-exchange barriers for methane at selected isolated Brønsted sites in zeolites FAU, MFI, BEA, ERI, and CHA are studied by combined quantum-chemicalclassical (QM/MM) calculations in an attempt to understand the factors that determine the reactivity at these Brønsted sites. The barrier of the D/H-exchange… (More)

- Martin Winger, Daniel Trzesniak, +5 authors Alex H. de Vries
- 2010

In a recent study published in this journal, Winger et al. investigate the magnitude of the time step to integrate the equations of motion in simulations with the coarse-grained MARTINI force field, using an implementation of MARTINI in the GROMOS software. Based primarily on the drift in temperature and the magnitude of the energy fluctuations in bulk… (More)

- Paul Sherwood, Alex H. de Vries, +4 authors Ian H. Hillierb
- 1998

The use of bare cluster models to understand the nature of zeoliteÈsubstrate interactions may be improved to take account of the environment of the acid site. We consider two models for introducing the electrostatic BrÔnsted e†ects of the zeolite lattice. The Ðrst involves generating a specialised correction potential by Ðtting a non-periodic array of ca.… (More)

The Langevin thermostat does not reproduce the correct hydrodynamics, i.e., the hydrodynamic interactions are unphysically screened. To correctly describe hydrodynamic interactions, we have to use the DPD thermostat1,2 instead. The DPD thermostat satisfies Newton’s third law by construction and owing to mass, momentum and temperature conservation,… (More)

The absorption edge in Mn K-edge X-ray absorption spectra of manganese oxide compounds shows a shift of several electronvolts in going from MnO through LaMnO3 to CaMnO3. On the other hand, in X-ray photoelectron spectra much smaller shifts are observed. To identify the mechanisms that cause the observed chemical shifts, 1s ionization as well as 1s 3 “4p”… (More)