Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis

In order to get the dynamic molecule model from the static one, the molecular dynamics (MD) simulation needs to be performed. Some software sets such as GROMACS are used for that purpose. Unfortunately they lack GUI. The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from...

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Detalles Bibliográficos
Autores principales: Makarewicz, Tomasz, Kaźmierkiewicz, Rajmund
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2016
Materias:
Software Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842225/
https://www.ncbi.nlm.nih.gov/pubmed/27107576
http://dx.doi.org/10.1007/s00894-016-2982-4
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author Makarewicz, Tomasz
Kaźmierkiewicz, Rajmund
author_facet Makarewicz, Tomasz
Kaźmierkiewicz, Rajmund
author_sort Makarewicz, Tomasz
collection PubMed
description In order to get the dynamic molecule model from the static one, the molecular dynamics (MD) simulation needs to be performed. Some software sets such as GROMACS are used for that purpose. Unfortunately they lack GUI. The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from the PyMOL software by GUI-based interface of GROMACS tools. This paper describes many improvements introduced into the Dynamics PyMOL plugin 2.0 including: an integration with ProDy library, possibility to use the implicit solvents, an ability to interpret the MD simulations, and implementation of some more GROMACS functionality.
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spelling pubmed-48422252016-05-16 Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis Makarewicz, Tomasz Kaźmierkiewicz, Rajmund J Mol Model Software Report In order to get the dynamic molecule model from the static one, the molecular dynamics (MD) simulation needs to be performed. Some software sets such as GROMACS are used for that purpose. Unfortunately they lack GUI. The Dynamics PyMOL plugin allows researcher to perform MD simulations directly from the PyMOL software by GUI-based interface of GROMACS tools. This paper describes many improvements introduced into the Dynamics PyMOL plugin 2.0 including: an integration with ProDy library, possibility to use the implicit solvents, an ability to interpret the MD simulations, and implementation of some more GROMACS functionality. Springer Berlin Heidelberg 2016-04-23 2016 /pmc/articles/PMC4842225/ /pubmed/27107576 http://dx.doi.org/10.1007/s00894-016-2982-4 Text en © The Author(s) 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Software Report
Makarewicz, Tomasz
Kaźmierkiewicz, Rajmund
Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
title Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
title_full Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
title_fullStr Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
title_full_unstemmed Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
title_short Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
title_sort improvements in gromacs plugin for pymol including implicit solvent simulations and displaying results of pca analysis
topic Software Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842225/
https://www.ncbi.nlm.nih.gov/pubmed/27107576
http://dx.doi.org/10.1007/s00894-016-2982-4
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