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Article . 2016 . Peer-reviewed
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SIRAH tools: mapping, backmapping and visualization of coarse-grained models

Authors: Matías R. Machado; Sergio Pantano;

SIRAH tools: mapping, backmapping and visualization of coarse-grained models

Abstract

Abstract Summary: Coarse-grained (CG) models reduce the cost of molecular dynamics simulations keeping the essence of molecular interactions. Still, the diversity of CG representations (sizes, connectivity, naming, etc.) hampers the handling and visualization of such models. SIRAH Tools comprises a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes, write GROMACS’ topological information at any resolution into PSF format and a VMD plugin to visualize, analyze and retrieve pseudo-atomistic information from CG trajectories performed with the SIRAH force field. These tools facilitate the use of intricate CG force fields outside the small developer’s community. Availability and implementation: Different utilities of SIRAH Tools are written in Perl, Tcl, or R. Documentation and source codes are freely distributed at http://www.sirahff.com. Contact: mmachado@pasteur.edu.uy or spantano@pasteur.edu.uy

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Keywords

Molecular Dynamics Simulation

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
111
Top 1%
Top 10%
Top 1%
gold