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Protocols

GROMACS specifications

Information


Unique identifier OMICS_05081
Name GROMACS
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

Subtool


  • g_wham

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Versioning


No version available

Documentation


Maintainer


  • person_outline GROMACS Team

Additional information


https://github.com/GromPy/GromPy

Publications for GROMACS

GROMACS citations

 (1608)
call_split

Ion–ion interactions in the denatured state contribute to the stabilization of CutA1 proteins

2018
Sci Rep
PMCID: 5955972
PMID: 29769700
DOI: 10.1038/s41598-018-25825-7
call_split See protocol

[…] mutant 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, w […]

call_split

Structural basis of actin monomer re charging by cyclase associated protein

2018
Nat Commun
PMCID: 5951797
PMID: 29760438
DOI: 10.1038/s41467-018-04231-7
call_split See protocol

[…] plex 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); […]

call_split

Clinically relevant mutations in the ABCG2 transporter uncovered by genetic analysis linked to erythrocyte membrane protein expression

2018
Sci Rep
PMCID: 5945641
PMID: 29749379
DOI: 10.1038/s41598-018-25695-z
call_split See protocol

[…] Three 100 ns long MD simulations were performed with the wild type and mutant NBDs using GROMACS with CHARMM36m force field,. For simulation details see the Supplementary materials. Analysis was performed by employing GROMACS tools, VMD Network Wizard Plugin, and the MDAnalysis Python pac […]

call_split

Identification and characterization of smallest pore forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109

2018
BMC Biochem
PMCID: 5944148
PMID: 29743008
DOI: 10.1186/s12858-018-0093-9
call_split See protocol

[…] tool [] without prior structural information. Both channels were simulated in a POPE bilayer containing a 1 M KCl solution (hexamer system about 66.000 atoms, octamer system about 90.000 atoms) using GROMACS 5.1.2 [] and the CHARMM36 force field [, ]. Long-range electrostatic potentials beyond the cut-off of 12 Å were computed using the particle mesh Ewald algorithm []. Lennard-Jones potentials we […]

library_books

Investigation of immunogenic properties of Hemolin from silkworm, Bombyx mori as carrier protein: an immunoinformatic approach

2018
Sci Rep
PMCID: 5934409
PMID: 29725106
DOI: 10.1038/s41598-018-25374-z

[…] he TLRs. We have also used B cell and T cell prediction tools to analyze the antigenic properties of hemolin. The stability of the TLR–hemolin complex was studied using molecular dynamics study using GROMACS. […]

library_books

In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways

2018
Sci Rep
PMCID: 5932038
PMID: 29720700
DOI: 10.1038/s41598-018-25061-z

[…] All MD simulations were carried out using the software package Gromacs 5.1– and the CHARMM36 force field–. The system was propagated in time using the leap frog integrator with a time step of 2 fs, with the only exception being the first equilibration run, in whi […]

Citations

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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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