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.
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