Journal ArticleDOI
LINCS : A linear constraint solver for molecular simulations
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Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules.Abstract:
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 multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. (C) 1997 John Wiley & Sons, Inc.read more
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
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.
Journal ArticleDOI
GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Journal ArticleDOI
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark Abraham,Teemu Murtola,Roland Schulz,Roland Schulz,Szilárd Páll,Jeremy C. Smith,Jeremy C. Smith,Berk Hess,Erik Lindahl,Erik Lindahl +9 more
TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.
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g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
TL;DR: A new tool, g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described, and the calculated interaction energy of 37 structurally diverse HIV-1 protease inhibitor complexes is compared.
Journal ArticleDOI
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
TL;DR: The parallel linear constraint solver (P-LINCS) is presented, which allows the constraining of all bonds in macromolecules and the energy conservation properties of (P-)LINCS are assessed in view of improvements in the accuracy of uncoupled angle constraints and integration in single precision.
References
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Journal ArticleDOI
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
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.
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GROMACS: A message-passing parallel molecular dynamics implementation
TL;DR: A parallel message-passing implementation of a molecular dynamics program that is useful for bio(macro)molecules in aqueous environment is described and can handle rectangular periodic boundary conditions with temperature and pressure scaling.
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SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
TL;DR: In this article, an analytical algorithm called SETTLE for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented, which is based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE.
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Constrained molecular dynamics: Simulations of liquid alkanes with a new algorithm
TL;DR: In this article, the authors present an algorithm for molecular dynamics simulation involving holonomic constraints using Gauss' principle of least constraint, using a fast exact solution for constraint forces and a new procedure to correct for accumulating numerical errors.
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Symplectic Numerical Integrators in Constrained Hamiltonian Systems
TL;DR: In this article, the authors investigated the symplecticness of numerical integrators for constrained dynamics, such as occur in molecular dynamics when bond lengths are made rigid in order to overcome stepsize limitations due to the highest frequencies.