Parameterization of the Gay-Berne coarse-grained potential from atomistically detailed anisotropic free energy volumes

Simulating a system of 300,000+ atoms, such as an explicitly solvated protein using all atom molecular dynamics on the microsecond time-scale, would require an enormous amount of computing power and specialized software, even with which would still require months of computing time. However, if the atomic degrees of freedom of the system can be reduced (or averaged) in some physically intuitive manner, while still retaining a connection with the underlying atomistic detail, microsecond simulations could be achieved within weeks or days. Coarse-graining, a sub-class of mesoscale modelling, is used to represent molecules in a reduced form as either regular spheroids (ellipsoids) or as continuum models, using specialized interaction potentials. The Gay-Berne is a one such coarse-grain potential, which has been particularly successful in that it has been used in modelling of liquid crystals, protein dynamics and lipid membrane and micelle formation...

Grantor dc:publisher.institution

Department of Chemistry

Year dc:date.issued

2012

Author dc:creator

• Gamieldien, Mogamat Riedaa

Advisor dc:contributor.advisor

• Naidoo, Kevin J

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/11427/10567

OAI identifier oai:identifier

oai:open.uct.ac.za:11427/10567