[gmx-users] simulating hydrocarbons in water

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 10 14:51:26 CEST 2007

Adam Fraser wrote:
> Hello,
> I'm very new to Gromacs, and I am interested in simulating the 
> interactions of 2 hexadecane (C16H34) molecules in water (SPC/E 
> specificall).  I've spent some time experimenting with tutorials in 
> Gromacs, but I've found little help in non-protein simulations like this 
> one.
> I've built topologies for hexadecane compatible with NAMD, so I figure I 
> should be able to do the same in Gromacs but I'm fuzzy on how to go 
> about doing so (what files to edit).  I was also hoping to get some 
> input on which forcefield would be best for this sort of system.
> I'd greatly appreciate it if someone could give me some pointers on how 
> to get started here.
> Thanks very much,
> Adam
if you have a pdb file you can run x2top (3.3.2 only).

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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

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