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Protocols

GROMOS specifications

Information


Unique identifier OMICS_05080
Name GROMOS
Alternative name GROningen MOlecular Simulation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline GROMOS Team

Publication for GROningen MOlecular Simulation

GROMOS citations

 (31)
library_books

Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities

2018
Front Pharmacol
PMCID: 5928326
PMID: 29740321
DOI: 10.3389/fphar.2018.00395

[…] en, ), OPLS-AA (Jorgensen et al., ), and GAFF (Wang et al., ). While these force fields parameterized their electrostatic terms using ab initio calculations, the GROMOS force fields (derived from the Groningen Molecular Simulation package) used free-energy of solvation as target (Daura et al., ; Oostenbrink et al., ) to empirically assign atomic partial charges. Thus, in this work, we have chosen […]

library_books

Interpreting the Mechanism of APOE (p.Leu167del) Mutation in the Incidence of Familial Hypercholesterolemia; An In silico Approach

2017
PMCID: 5688386
PMID: 29204218
DOI: 10.2174/1874192401711010084

[…] follow-up analysis.Predicted reference models of APOE and LDLR were subsequently subjected to energy minimization using DeepView-Swiss PDB Viewer (http://spdbv.vital-it.ch/). This software depends on GROningen MOlecular Simulation (GROMOS) 96 force field techniques to release local constraints at their local residues []. It is also noteworthy that the p.Leu167del mutation was manually curated in t […]

library_books

Genetic Epidemiology of Glucose 6 Dehydrogenase Deficiency in the Arab World

2016
Sci Rep
PMCID: 5112515
PMID: 27853304
DOI: 10.1038/srep37284

[…] The protein structures of the native and mutant were used as the initiation of Molecular Dynamics Simulation. The simulation for the protein structure was performed using Gromacs 4.5.6 package with GROMOS96 43a1 force field. Initially, the protein structure was solvated in a cubic box with 10 Å radii. Further, using “genion” tool, the system was neutralised by adding Chlorine ions as there was a […]

library_books

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

2016
J Chem Inf Model
PMCID: 5039763
PMID: 27559757
DOI: 10.1021/acs.jcim.6b00399

[…] s A, B, and C in this equation. We chose the Pardi parameters (A = 6.4, B = −1.4, and C = 1.9), which have been used previously for the protein backbone in the context of simulation studies using the GROMOS force field., Since Hα is not represented by an actual atom in the GROMOS force field, we approximate the HN–N–Cα–Hα dihedral angle by subtracting 60° from ϕ, making use of the planarity of the […]

call_split

In Silico Design of a Chimeric Protein Containing Antigenic Fragments of Helicobacter pylori; A Bioinformatic Approach

2016
PMCID: 4899534
PMID: 27335622
DOI: 10.2174/1874285801610010097
call_split See protocol

[…] geometry of the model, PROCHEK server (swissmodel.expasy.org/workspace). For picturing of three dimensional models of the chimeric protein, Rasmol tool and Accelrys Discovery Studio1.7 were used. The GROMOS96 implemented in SWISS MODEL software helps to reduce the bond str etc. h energy of the modeled protein []. […]

library_books

Proton currents constrain structural models of voltage sensor activation

2016
eLife
PMCID: 5065317
PMID: 27572256
DOI: 10.7554/eLife.18017.029

[…] m () was used throughout to constrain bond lengths. The time step for integration in both simulations was 2 fs. All analyses used GROMACS tools and locally written code.The final snapshots from Hv1 D GROMOS96 MD simulation was used as the template for the introduction of the R1H mutation using the Mutator plugin (VMD 1.9.2). The final snapshot of the GROMOS96 MD of the Hv1 B model structure () was […]

Citations

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GROMOS institution(s)
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, Zürich, Switzerland

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