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Journal ArticleDOI: 10.1002/JCC.20291

GROMACS: Fast, flexible, and free

01 Dec 2005-Journal of Computational Chemistry (Wiley)-Vol. 26, Iss: 16, pp 1701-1718
Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

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Topics: Software suite (50%)
Citations
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Open accessJournal ArticleDOI: 10.1021/CT700301Q
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

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  • Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
    Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
  • Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
    Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
  • Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
    Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
  • Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
    Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
  • Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
    Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
  • + 2

Topics: Particle Mesh (50%)

12,609 Citations


Open accessJournal ArticleDOI: 10.1016/J.SOFTX.2015.06.001
Mark Abraham1, Teemu Murtola2, Roland Schulz3, Roland Schulz4  +6 moreInstitutions (4)
01 Sep 2015-SoftwareX
Abstract: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, prepa ...

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8,050 Citations


Open accessJournal ArticleDOI: 10.1002/JCC.21287
Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

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5,997 Citations


Open accessJournal ArticleDOI: 10.1021/JP071097F
Abstract: We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.

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Topics: Lipid bilayer mechanics (56%), Bilayer (52%)

3,886 Citations


Journal ArticleDOI: 10.1002/JCC.20945
Abstract: CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery.

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2,976 Citations


References
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Journal ArticleDOI: 10.1063/1.445869
Abstract: Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.

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Topics: Water model (53%), Solvent models (52%), Water dimer (51%) ...read more

29,424 Citations


Open accessJournal ArticleDOI: 10.1063/1.448118
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

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  • TABLE I. Thermodynamic quantities for water using coupling to a P, T bath.'
    TABLE I. Thermodynamic quantities for water using coupling to a P, T bath.'
  • FIG. 3. Autocorrelation function and spectral density for center-of-mass velocity of water molecules for various values of coupling constants to temperature bath (TT) and pressure bath (rp). All curves coincide for TT>O.1 ps and Tp>O.1 ps (drawn curves). Broken curves: TT = Tp = 0.01 ps.
    FIG. 3. Autocorrelation function and spectral density for center-of-mass velocity of water molecules for various values of coupling constants to temperature bath (TT) and pressure bath (rp). All curves coincide for TT>O.1 ps and Tp>O.1 ps (drawn curves). Broken curves: TT = Tp = 0.01 ps.
  • FIG. I. Fluctuations of kinetic, total, and potential energy in two 1 ps molecular dynamics runs of216 water molecules, starting from the same initial conditions (T = 300 K). a isochoric, microcanonical simulation (T T = 00), b isochoric simulation with weak coupling to constant temperature bath (T T = 0.4 ps). The vertical scale respresents I kJ Imol per division. Horizontal lines represent averages for each curve.
    FIG. I. Fluctuations of kinetic, total, and potential energy in two 1 ps molecular dynamics runs of216 water molecules, starting from the same initial conditions (T = 300 K). a isochoric, microcanonical simulation (T T = 00), b isochoric simulation with weak coupling to constant temperature bath (T T = 0.4 ps). The vertical scale respresents I kJ Imol per division. Horizontal lines represent averages for each curve.
  • FIG. 2. Root means square fluctuations in kinetic, total, and potential energies, measured over several 0.1 ps simulations of liquid water.
    FIG. 2. Root means square fluctuations in kinetic, total, and potential energies, measured over several 0.1 ps simulations of liquid water.
Topics: Coupling (52%), Constant (mathematics) (52%), Non-equilibrium thermodynamics (51%) ...read more

22,197 Citations


Open accessJournal ArticleDOI: 10.1063/1.464397
Tom Darden1, Darrin M. York1, Lee G. Pedersen1Institutions (1)
Abstract: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.

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Topics: Ewald summation (69%), P3M (64%), Particle Mesh (51%)

20,639 Citations


Open accessBook
Michael P. Allen1, D. J. TildesleyInstitutions (1)
11 Feb 1988-
Abstract: Introduction Statistical mechanics Molecular dynamics Monte Carlo methods Some tricks of the trade How to analyse the results Advanced simulation techniques Non-equilibrium molecular dynamics Brownian dynamics Quantum simulations Some applications Appendix A: Computers and computer simulation Appendix B: Reduced units Appendix C: Calculation of forces and torques Appendix D: Fourier transforms Appendix E: The gear predictor - corrector Appendix F: Programs on microfiche Appendix G: Random numbers References Index.

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20,549 Citations


Open access
01 Jan 1994-
Abstract: Note: Includes bibliographical references, 3 appendixes and 2 indexes.- Diskette v 2.06, 3.5''[1.44M] for IBM PC, PS/2 and compatibles [DOS] Reference Record created on 2004-09-07, modified on 2016-08-08

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Topics: IBM PC compatible (59%)

19,744 Citations


Performance
Metrics
No. of citations received by the Paper in previous years
YearCitations
202236
20211,264
20201,107
2019915
2018938
2017812