GROMACS pipeline

GROMACS specifications


Unique identifier OMICS_05081
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
Parallelization CUDA
License GNU General Public License version 2.0
Computer skills Advanced
Version 2018
Stability Stable
Maintained Yes


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Additional information

Publications for GROMACS

GROMACS citations

PMCID: 5940241

[…] the talin rod subdomains in order to form the disulphide bonds (clamps) preventing the unfolding of 3-helix state, were designed and mutated using pymol., md and smd simulations were performed using gromacs ver 2016.1[49,50] at the sisu supercomputer, csc, finland. the charmm27 force field[51] and explicit tip3p water model[52] in 0.15 m kcl solution were used and the total charge of the system […]

PMCID: 5928492

[…] in the initial velocity distributions to get a simple estimate of the statistical fluctuations between trajectories. data are saved every 4 ps for further analysis. using the internal tools of gromacs, we measured rmsds of the cα atoms, secondary structure contents, contact distances, and hydrogen bonding. configurations are visualized using pymol54 and vmd., the supporting information […]

PMCID: 5842552

[…] while the topologies of the protein were generated employing chemistry at harvard macromolecular mechanics force-field (charmm ff) [51–54] implemented in groningen machine for chemical simulations (gromacs) 5.0.6 [55]. dodecahedron box was obtained and was solvated with three-site transferable intermolecular potential (tip3p) water model followed by neutralizing the system with the counter […]

PMCID: 5664374

[…] selected compounds and to evaluate the dynamic behaviour of the prospective drug molecules in the binding site pocket, they were subjected to md simulation along with the reference compound using gromacs 4.5.7 [25–27], employing charmm27 [25] force field. ligand topologies were generated using swissparam [28]. corresponding counterions were added to neutralize the solvated tip3p water model […]

PMCID: 5560777

[…] before the 400-ns unrestrained production simulations. we then repeated the 400-ns production simulations using different initial velocities for both systems. simulations were conducted using gromacs 4.6 (hess et al., 2008) with a 2 fs integration time step and visualized using vmd, pymol (humphrey et al., 1996), or discovery visualizer 4.0 (accelrys)., mouse girk2 (containing amino acids […]

GROMACS institution(s)
Theoretical Biophysics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden; Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA; Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
GROMACS funding source(s)
This work was supported by the European Research Council (258980), the Swedish Research Council (2013-5901) the Swedish e-Science Research Center, the ScalaLife EU infrastructure (261523), the EU FP7 CRESTA project (287703), Intel Corporation and the ORNL Adaptive Biosystems Imaging project funded by the Biological and Environmental Research of the Office of Science of the U.S. Department of Energy.

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