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J Comput Chem. 2012 Jan 30;33(3):340-53. doi: 10.1002/jcc.21954. Epub 2011 Nov 11.

New functionalities in the GROMOS biomolecular simulation software.

Author information

1
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland.

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.

PMID:
22076815
DOI:
10.1002/jcc.21954
[Indexed for MEDLINE]

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