[gmx-users] New user, familiar with MD, unfamiliar with GROMACS, want to run simulation of protein in membrane

[David van der Spoel]

maria goranovic wrote:
> Hi All,
> 
> I am a brand new user of GROMACS, and want to run a simulation of a 
> protein embedded in a large POPC lipid bilayer. I am familiar with MD in 
> general (have used NAMD before).
> 
> It would be very helpful if you could please advise me where to start ? 
> Specifically:
> 
> - which force field versions to use ? I understand there are various 
> versions within GROMACS ?
> - how to setup systems ?
> 
> I am sure this must be a fairly common question, and a repository with 
> the necessary directions probably exists for new users like me ?
> 
> Thank you very much in advance for your help,
> 
check out wiki.gromacs.org
search web for peter tieleman and download his membrane input files.
> Sincerely,

> 
> -Maria
> 
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se