GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

References

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	Year	Citations
VMD: Visual molecular dynamics William Humphrey, Andrew Dalke, Klaus Schulten Journal of Molecular Graphics EngineeringVisual Molecular DynamicsMolecular BiologyComputational ChemistryMolecular Dynamics	1996	64.1K
Fast Parallel Algorithms for Short-Range Molecular Dynamics Steven J. Plimpton Journal of Computational Physics EngineeringFast Parallel AlgorithmsParallel ProgrammingComputational ChemistryParallel Computing	1995	43.6K
Particle mesh Ewald: An <i>N</i>⋅log(<i>N</i>) method for Ewald sums in large systems Tom Darden, Darrin M. York, Lee G. Pedersen The Journal of Chemical Physics Numerical AnalysisEngineeringElectrostatic EnergiesParticle MethodComputational Chemistry	1993	29.8K
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Jean-Paul Ryckaert, Giovanni Ciccotti, Herman J. C. Berendsen Journal of Computational Physics Numerical AnalysisCartesian EquationsEngineeringPhysicsNumerical Integration	1977	21.1K
GROMACS: Fast, flexible, and free David van der Spoel, Erik Lindahl, Berk Hess, Journal of Computational Chemistry	2005	18.4K
Canonical sampling through velocity rescaling Giovanni Bussi, Davide Donadio, Michele Parrinello The Journal of Chemical Physics EngineeringCanonical DistributionNew Molecular DynamicsParticle MethodComputational Chemistry	2007	17.5K
Scalable molecular dynamics with NAMD J. C. Phillips, Rosemary Braun, Wei Wang, Journal of Computational Chemistry	2005	17.1K
LINCS: A linear constraint solver for molecular simulations Berk Hess, Henk Bekker, Herman J. C. Berendsen, Journal of Computational Chemistry Linear Constraint SolverBond ConstraintsMolecular SciencesShake AlgorithmEngineering	1997	16.6K
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation Berk Hess, Carsten Kutzner, David van der Spoel, Journal of Chemical Theory and Computation Cluster ComputingEngineeringMolecular BiologyComputational ChemistryScalable Molecular Simulation	2008	15.8K
<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, Journal of Computational Chemistry EngineeringMolecular BiologyEmpirical Energy FunctionComputational ChemistryEnergy Minimization	1983	14.9K

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