Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 33, Issue 3, Pages 340-353Publisher
WILEY
DOI: 10.1002/jcc.21954
Keywords
GROMOS; polarizability; switching function; SASA; VOL; coarse-graining; nonequilibrium dynamics
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Funding
- Swiss National Science Foundation, National Center of Competence in Reserch in structural biology [200020-121913]
- European Research Council [228076]
- Sino-Swiss Science and Technology Cooperation Program [IZLCZ2-123884 (Swiss), GJHZ0906 (Chinese)]
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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. (C) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012
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