GROMACS protocols

GROMACS computational protocol

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 IN pipelines

PMCID: 5796906
PMID: 29434596
DOI: 10.3389/fimmu.2018.00075

[…] and trajectories were saved every 2 ps. data analysis was performed using xmgrace,1 vmd 1.9.2 (31), pymol 1.7 (schrödinger, llc, new york, ny, usa), dsv 4.0, and other analysis programs available in gromacs. the area per lipid (apl) was calculated using gridmat-md (32)., the binding free energies (bfe) between different segments of the tirap and pi molecules were calculated using the mm/pbsa […]

PMCID: 5813003
PMID: 29445244
DOI: 10.1038/s41598-018-21357-2

[…] permeability was obtained simply by counting the number of permeation events per pore50., vmd51 was used for analysis and trajectory visualization, including rendering of trajectory snapshots. the gromacs tools and mdanalysis49 libraries were used in the analysis scripts., the free energy along the pore axis for ammonia was calculated using awh52,53. awh is an enhanced sampling algorithm […]

PMCID: 5923327
PMID: 29670004
DOI: 10.3390/toxins10040161

[…] 1.8.1, san francisco, ca, usa, 2013) [40]., for the molecular dynamics simulations, the amidated model topologies were defined by charmm27 force field [41]. the simulations were performed using gromacs 5.1.4 software (san francisco, ca, usa, 2016) [42] with the water explicit model tip3p and with 50%tfe solution. the models were submitted to energy and temperature minimization […]

PMCID: 5397185
PMID: 28088759
DOI: 10.1093/nar/gkw1355

[…] this work., during production runs, data was typically collected every 1 ps, which allowed us to study infrequent, but fast movements. geometrical analysis were carried out with ambertools 14 (28), gromacs tools, mdweb (44,45,46), naflex (47) and the curves+ package (48). as in our recent work (18), the 3d-rism model (37, for details see 11) was used to compute the saxs-waxs spectra […]

PMCID: 5419745
PMID: 28398197
DOI: 10.7554/eLife.16059.028

[…] from the averaging over a finite number of replicas as well as the error estimate for random, systematic and the intrinsic error of the forward model (i.e. camshift). all simulations were run in gromacs (pronk et al., 2013) using plumed 2 (tribello et al., 2014). van der waals and coulomb interactions were implemented with a cutoff at 0.9 nm, and long-range electrostatic effects were treated […]

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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