Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born (Q35948015)

11 August 2017

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born (English)

1 reference

11 August 2017

Mark J Williamson

0 references

Andreas W Götz

1 reference

11 August 2017

Dong Xu

1 reference

11 August 2017

Duncan Poole

1 reference

11 August 2017

Scott Le Grand

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11 August 2017

Ross C Walker

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11 August 2017

26 March 2012

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Journal of Chemical Theory and Computation

11 August 2017

1 reference

11 August 2017

1 reference

11 August 2017

1 reference

11 August 2017

1542-1555

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Generalized Born model with a simple, robust molecular volume correction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Long-timescale molecular dynamics simulations of protein structure and function.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Accelerating molecular dynamic simulation on graphics processing units

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Accelerating molecular modeling applications with graphics processors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Simulating movement of tRNA into the ribosome during decoding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

The Amber biomolecular simulation programs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Molecular dynamics and protein function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Structure of ubiquitin refined at 1.8 A resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Three-dimensional structure of ubiquitin at 2.8 A resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Dynamics of folded proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Determining the Numerical Stability of Quantum Chemistry Algorithms.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Analytical electrostatics for biomolecules: beyond the generalized Born approximation

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Molecular dynamics simulations of hydrophobic collapse of ubiquitin

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348677

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

24 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22582031

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Theory and applications of the generalized Born solvation model in macromolecular simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22582031

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

FASTRUN: a special purpose, hardwired computer for molecular simulation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22582031

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT200909J

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

22582031

1 reference