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
Descripción
Sumario: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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