[gmx-users] simulating hydrocarbons in water

[Adam Fraser]

Yes I tried this and it doesn't work for me.  I get:

Fatal error:
Library file ffG53a6.n2t not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)

Also, doesn't x2top take in a gro file?  (not a pdb)  I wrote a script that
converts pdb to gro, and I still get the above error.

-Adam

On 10/10/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> 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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> >
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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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