| Title | New functionalities in the GROMOS biomolecular simulation software |
| Publication Type | Miscellaneous |
| Year of Publication | 2012 |
| Authors | Kunz, A-PE, Allison JR, Geerke DP, Horta BAC, Hünenberger PH, Riniker S, Schmid N, van Gunsteren WF |
| ISBN Number | 1096-987X |
| Keywords | coarse-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 |
| URL | http://dx.doi.org/10.1002/jcc.21954 |
New functionalities in the GROMOS biomolecular simulation software
Publications by Jane Allison
2012.
Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol.
The Journal of Chemical Physics.
136:
054505-11
2012.
New functionalities in the GROMOS biomolecular simulation software.
Journal of Computational Chemistry.
33:
340-353
2011.
Current computer modeling cannot explain why two highly similar sequences fold into different structures.
Biochemistry.
50:
10965-10973
2011.
A refined, efficient mean solvation force model that includes the interior volume contribution.
The Journal of Physical Chemistry B.
115:
4547-4557
2011.
GROMOS++ software for the analysis of biomolecular simulation trajectories.
Journal of Chemical Theory and Computation.
7:
3379-3390
2011.
Biomolecular structure refinement using the GROMOS simulation software.
Journal of Biomolecular NMR.
51:
265-281
