OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation (Q30415382)

14 August 2017

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation (English)

1 reference

14 August 2017

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Michael R Shirts

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Lee-Ping Wang

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Vijay S Pande

1 reference

14 August 2017

Kyle A Beauchamp

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14 August 2017

Peter Eastman

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14 August 2017

John D Chodera

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14 August 2017

Mark S Friedrichs

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14 August 2017

Randall J Radmer

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14 August 2017

Christopher M Bruns

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14 August 2017

Joy P Ku

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14 August 2017

Thomas J Lane

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14 August 2017

Diwakar Shukla

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14 August 2017

Tony Tye

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14 August 2017

Mike Houston

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14 August 2017

Timo Stich

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14 August 2017

Christoph Klein

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14 August 2017

18 October 2012

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Journal of Chemical Theory and Computation

14 August 2017

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14 August 2017

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14 August 2017

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14 August 2017

461-469

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Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Generalized Born model with a simple, robust molecular volume correction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Efficient stochastic thermostatting of path integral molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

CHARMM: the biomolecular simulation program

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Accelerating molecular dynamic simulation on graphics processing units

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Statistically optimal analysis of samples from multiple equilibrium states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Accelerating molecular modeling applications with graphics processors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Comparison of multiple Amber force fields and development of improved protein backbone parameters

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Scalable molecular dynamics with NAMD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Quantum statistics and classical mechanics: real time correlation functions from ring polymer molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Empirical force fields for biological macromolecules: overview and issues.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Exploring protein native states and large-scale conformational changes with a modified generalized born model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Structure of ubiquitin refined at 1.8 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3539733

The generalized Born/volume integral implicit solvent model: estimation of the free energy of hydration using London dispersion instead of atomic surface area

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23316124

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT300857J

1 reference

14 August 2017

1 reference

14 August 2017

PubMed publication ID

23316124

1 reference