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Jean-Paul Ryckaert

Bio: Jean-Paul Ryckaert is an academic researcher from Université libre de Bruxelles. The author has contributed to research in topics: Molecular dynamics & Shear flow. The author has an hindex of 31, co-authored 94 publications receiving 21103 citations. Previous affiliations of Jean-Paul Ryckaert include Heriot-Watt University & University of Paris.


Papers
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Journal ArticleDOI
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.

18,394 citations

Journal ArticleDOI
TL;DR: In this paper, a semi-rigid model with fixed C-C bonds and angles was used for simulation of liquid systems of n-alkanes and the results of two different simulations of nbutane and of one simulation of ndecane were analyzed.
Abstract: The method of molecular dynamics is applied to the simulation of liquid systems of n-alkanes. The model used is a semi-rigid one with fixed C—C bonds and C—C—C angles. In addition to the static and dynamic properties usually deduced for monatomic fluids from such computer experiments, the configurational properties and the internal relaxation behaviour of the alkane chain are also studied. The results of two different simulations of n-butane and of one simulation of n-decane are analysed. The usefulness and the limitations of such computer experiments are discussed briefly.

615 citations

Journal ArticleDOI
TL;DR: The self-diffusion coefficient of n-butane is approximately 6.0 × 10−5 cm2/s and the corresponding velocity autocorrelation function displays practically no cage effect, differing markedly from argon and other simple fluids.

578 citations

Journal ArticleDOI
TL;DR: A review of the method of constraints, devised to carry out Molecular Dynamics simulations of complex molecular systems with some internal degrees of freedom frozen, in terms of atomic Cartesian coordinates, and deriving the statistical-mechanical formalism for these systems.

408 citations

Journal ArticleDOI
TL;DR: The dynamics of rigid polyatomic systems, either molecules or rigid portions of large molecules, is described by cartesian equations of motion for its atoms as discussed by the authors. But this is not the case in the case of the present paper.
Abstract: The dynamics of rigid polyatomic systems, either molecules or rigid portions of large molecules, is described by cartesian equations of motion for its atoms. In comparison with the original version of the method of constraints

311 citations


Cited by
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Journal ArticleDOI
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Abstract: In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath

25,256 citations

Journal ArticleDOI
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.

18,394 citations

Journal ArticleDOI
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

17,897 citations

Journal ArticleDOI
TL;DR: A new implementation of the molecular simulation toolkit GROMACS is presented which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines.
Abstract: Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

14,032 citations

Journal ArticleDOI
TL;DR: The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals.
Abstract: New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

13,164 citations