MkVsites: A tool for creating GROMACS virtual sites parameters to increase performance in all-atom molecular dynamics simulations.
GROMACS
molecular dynamics
sampling
timestep
Journal
Journal of computational chemistry
ISSN: 1096-987X
Titre abrégé: J Comput Chem
Pays: United States
ID NLM: 9878362
Informations de publication
Date de publication:
15 06 2020
15 06 2020
Historique:
received:
10
02
2020
revised:
11
03
2020
accepted:
14
03
2020
pubmed:
14
4
2020
medline:
14
4
2020
entrez:
14
4
2020
Statut:
ppublish
Résumé
The absolute performance of any all-atom molecular dynamics simulation is typically limited by the length of the individual timesteps taken when integrating the equations of motion. In the GROMACS simulation software, it has for a long time been possible to use so-called virtual sites to increase the length of the timestep, resulting in a large gain of simulation efficiency. Up until now, support for this approach has in practice been limited to the standard 20 amino acids however, shrinking the applicability domain of virtual sites. MkVsites is a set of python tools which provides a convenient way to obtain all parameters necessary to use virtual sites for virtually any molecules in a simulation. Required as input to MkVsites is the molecular topology of the molecule(s) in question, along with a specification of where to find the parent force field. As such, MkVsites can be a very valuable tool suite for anyone who is routinely using GROMACS for the simulation of molecular systems.
Identifiants
pubmed: 32282082
doi: 10.1002/jcc.26198
pmc: PMC7384070
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1564-1569Informations de copyright
© 2020 Wiley Periodicals, Inc.
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