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New functionalities in the GROMOS biomolecular simulation software

✍ Scribed by Anna-Pitschna E. Kunz; Jane R. Allison; Daan P. Geerke; Bruno A. C. Horta; Philippe H. Hünenberger; Sereina Riniker; Nathan Schmid; Wilfred F. van Gunsteren

Book ID
102306189
Publisher
John Wiley and Sons
Year
2011
Tongue
English
Weight
433 KB
Volume
33
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

Since the most recent description of the functionalities of the GROMOS software for biomolecular simulation in 2005 many new functions have been implemented. In this article, the new functionalities that involve modified forces in a molecular dynamics (MD) simulation are described: the treatment of electronic polarizability, an implicit surface area and internal volume solvation term to calculate interatomic forces, functions for the GROMOS coarse‐grained supramolecular force field, a multiplicative switching function for nonbonded interactions, adiabatic decoupling of a number of degrees of freedom with temperature or force scaling to enhance sampling, and nonequilibrium MD to calculate the dielectric permittivity or viscosity. Examples that illustrate the use of these functionalities are given. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012

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