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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: 5792426
PMID: 29346773
DOI: 10.1016/j.celrep.2017.12.075

[…] structure models were generated using i-tasser (). ssp2 model was further regularized by 1 ns molecular dynamics in explicit solvent followed by energy minimization (gromacs 2016.3; ). structural alignments were performed in pymol (version; schrodinger)., quantitative data were analyzed and presented using graphpad prism, and pairwise comparison […]

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

[…] and trajectories were saved every 2 ps. data analysis was performed using xmgrace, vmd 1.9.2 (), 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 ()., the binding free energies (bfe) between different segments of the tirap and pi molecules were calculated using the mm/pbsa […]

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

[…] were generated, and the top ranked prediction was chosen based on the highest zdock score (i.e., a statistical pair potential score of 1,564.68). energy minimization was carried out using the gromacs 5.1.4 simulation package () to relieve steric clashes between side chain and main chain atoms., the ntd (residues 1–78) was modeled using the threading-based i-tasser modeling server (). […]

PMCID: 5829529
PMID: 29527168
DOI: 10.3389/fphar.2018.00134

[…] according to previously published protocols (stitham et al., ; pérez-villa et al., ), each protein structure was first equilibrated by 100 ns explicit solvent molecular dynamics simulation using the gromacs4.6.7 program (pronk et al., ) and charmm27 force field (brooks et al., ). details of the molecular dynamics simulation setup were as previously described (li et al., ; xu et al., ). vs […]

PMCID: 5842552
PMID: 29514608
DOI: 10.1186/s12885-018-4050-1

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

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GROMACS in publications

PMCID: 5959319
DOI: 10.1126/sciadv.aar8521

[…] water model (). we refer to this combination as vdw-opc. parameters are available at md simulations were performed using the groningen machine for chemical simulations (gromacs) 4.6.7 software package (). ideal a-form, fully stacked initial conformations were generated using the make-na web server. the oligonucleotides were solvated in a truncated dodecahedric box […]

PMCID: 5955972
PMID: 29769700
DOI: 10.1038/s41598-018-25825-7

[…] also lacking sh groups with td = 113.3 °c (ec0vv = ec0sh_s11v/e61v), and an ionic mutant with td = 136.8 °c (ec0vv_6 = ec0vv_a39d/s48k/h72k/s82k/q87k/t88r)., md simulations were performed using gromacs software (ver. 4.5.5),. the missing atoms in the coordinate file of ec0sh (pdb id, 4y65), which are three n-terminal residues of the b subunit and eight n-terminal residues of the c subunit, […]

PMCID: 5955887
PMID: 29769636
DOI: 10.1038/s41598-018-26070-8

[…] 0 ns runs with gradually decreasing force constants (k = 500, 100, 50, 10 kj/mol/nm2). each of the 704 receptor/membrane complexes was then run for at least 5 µs. all simulations were performed using gromacs 5.0 and in the npt ensemble at 310 k and 1 bar. constant temperature and pressure were maintained using the velocity-rescale and berendsen algorithms, respectively. the coulombic interactions […]

PMCID: 5953967
PMID: 29765052
DOI: 10.1038/s41467-018-04330-5

[…] as starting points for ten statistically independent 10 ps long nve trajectories at each temperature, where the time step was 1 fs and double-precision was used for accurate energy conservation. the gromacs 5.0.4 simulation package was used for all trajectories. classical molecular dynamics simulations of water interacting via the mb-pol potential were also performed. mb-pol is a polarizable […]

PMCID: 5951797
PMID: 29760438
DOI: 10.1038/s41467-018-04231-7

[…] and determination of protonation states at ph = 6.8), chimera (placing hydrogens), vmd (protein structure building and visualization), and pytopol (protein topology conversion from charmm to the gromacs format). in all systems, e454 and h416 of the carp domain were protonated; n-terminus of actin was acetylated; the his73 residue of actin was methylated (parameters were obtained by analogy); […]

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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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