OpenMM protocols

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Information


Unique identifier OMICS_14094
Name OpenMM
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
Computer skills Advanced
Version 7.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Peter Eastman <>

Publications for OpenMM

OpenMM in pipelines

 (3)
2017
PMCID: 5585393
PMID: 28874689
DOI: 10.1038/s41598-017-09654-8

[…] using ccd and a final candidate gets selected using statistical potentials of mean force. the sidechain modelling is inspired by scwrl4. a final energy minimization is performed using the openmm molecular mechanics library. each model is annotated with the qs-score to the native structure and the set of features described in the text. to ensure an un-biased learning step, all models […]

2017
PMCID: 5703577
PMID: 29131852
DOI: 10.1371/journal.ppat.1006716

[…] the swiss-model template library and models were built using promod3 and alternatively promod-ii []. following loop and side chains modeling, a last energy minimization step is performed using the openmm [] molecular mechanics library., for structural analysis purposes two different models were chosen based on different template structures obtained from different experimental methods. firstly, […]

2015
PMCID: 4669690
PMID: 25950479
DOI: 10.1038/cddis.2015.110

[…] dynamics (mds) run in order to relax the potentially non-equilibrium structures. the md was prepared and performed using the gpu version of the gromacs suite of programs as implemented in the openmm zephyr package. average structures from second half of the simulations were further used for the docking study. the docking study of the mitoves, ttfa and ubiquinone ligands/inhibitors […]


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OpenMM in publications

 (36)
PMCID: 5806882
PMID: 29425231
DOI: 10.1371/journal.pone.0192736

[…] field for the protein degrees of freedom [], the gaff force field for the ligand degrees of freedom [], and the obc2 generalized-born implicit solvent model [,]. simulations were performed using the openmm simulation library [] with a non-bonded cut-off of 1 nanometer, a salt concentration of 150 mm, and hydrogen bond lengths constrained. equations of motion were integrated with a langevin […]

PMCID: 5772613
PMID: 29343704
DOI: 10.1038/s41467-017-02711-w

[…] initial structures of the helical core (residues 290–343) of the c-terminal domain of cdc37 were taken from the protein data bank (pdb id 2n5x). systems were built using charmm, but run with openmm using the charmm force field. three different systems were modeled, the unphosphorylated and y298 phosphorylated wild types, and the y298e mutant. systems were solvated in tip3p water boxes, […]

PMCID: 5849412
PMID: 29465396
DOI: 10.7554/eLife.32766.019

[…] only heavy atoms) was extracted from the structure and converted to a protonated tripos mol2 file using openeye toolkit oechem v2015.june (; ). the protein structure was then loaded as an openmm version 7.0.1 modeller object, and the protonated adp was reintroduced through conversion from mol2 to openmm format via mdtraj 1.4.2 (; )., simulations of phosphorylated wt aura in complex […]

PMCID: 5896879
PMID: 29638214
DOI: 10.7554/eLife.32963.032

[…] or dnacaa; the dna sequence used in the simulations contained nucleotides g5 – c18 from the crystal structure. the charmm 36 forcefield (; ; ; ; ) and charmm program (), with the charmm interface to openmm () to allow the use of nvidia graphical processing units (gpus), were used for all simulations. the starting structure was placed in a cubic solvent box with 8 nm side length containing water […]

PMCID: 5730859
PMID: 29217590
DOI: 10.15252/embj.201798083

[…] t al, )., polymer simulations of loop extrusion were performed as in flyamer et al (), but using updates to the simulation engine (fudenberg & imakaev, ). the simulation engine is built using the openmm‐polymer package which relies on openmm 7 (eastman et al, ). parameters for simulations were as follows: 2,000 md steps per loop extrusion step. simulations were performed using either n = 30,00 […]


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OpenMM institution(s)
Department of Chemistry, Stanford University, Stanford, CA, USA; Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, USA; Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Counsyl Research, South San Francisco, CA, USA; Department of Chemistry, University of California, Davis, CA, USA; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
OpenMM funding source(s)
This was supported by the NIH Roadmap for Medical Research Grant U54 GM072970, NIH grant R01-GM062868, the Sloan Kettering Institute, NIH grant P30 CA008748, and Starr Foundation grant I8-A8-058.

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