New functionalities in the GROMOS biomolecular simulation software

TitleNew functionalities in the GROMOS biomolecular simulation software
Publication TypeMiscellaneous
Year of Publication2012
AuthorsKunz, A-PE, Allison JR, Geerke DP, Horta BAC, Hünenberger PH, Riniker S, Schmid N, van Gunsteren WF
ISBN Number1096-987X
Keywordscoarse-graining, GROMOS, nonequilibrium dynamics, polarizability, SASA/VOL, switching function
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

URLhttp://dx.doi.org/10.1002/jcc.21954

Publications by Jane Allison

Müller, MM, Allison JR, Hongdilokkul N, Gaillon L, Kast P, van Gunsteren WF, Marlière P, Hilvert D. 2013. Directed Evolution of a Model Primordial Enzyme Provides Insights into the Development of the Genetic Code. PLoS Genet. 9: e1003187
Steiner, D, Allison J, Eichenberger A, van Gunsteren W. 2012. On the calculation of 3Jαβ-coupling constants for side chains in proteins. Journal of Biomolecular NMR. 53: 223-246
Riniker, S, Allison JR, van Gunsteren WF. 2012. On developing coarse-grained models for biomolecular simulation: a review. Physical Chemistry Chemical Physics. :
Kleinjung, J, Scott WRP, Allison J R, van Gunsteren WF, Fraternali F. 2012. Implicit solvation parameters derived from explicit water forces in large-scale Molecular Dynamics simulations. J. Chem. Theory Comput.. :
Allison, JR, Riniker S, van Gunsteren WF. 2012. Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol. The Journal of Chemical Physics. 136: 054505-11