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- 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)

- 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)

- M. Winger, D. Trzesniak, +5 authors Alex H. de Vries
- 2010

In a recent study published in this journal, Winger et al. 1 investigate the magnitude of the time step to integrate the equations of motion in simulations with the coarse-grained MARTINI force field, 2 using an implementation 3 of MARTINI in the GROMOS software. 4 Based primarily on the drift in temperature and the magnitude of the energy fluctuations in… (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)

Most analyses of circuit equations start with solving the steady-state (DC) solution. In several cases this can be very hard. We present a novel time domain source stepping procedure to obtain a DC solution of circuit equations. The source stepping procedure is automatically adap-tive. Controlled sources can be elegantly dealt with. The method can easily be… (More)

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