[gmx-users] simulating hydrocarbons in water

[Adam Fraser]

Much appreciated, works beautifully!

On 10/10/07, TJ Piggot <t.piggot at bristol.ac.uk> wrote:
>
> Just as a note editconf will covert a pdb to a gro file
>
> Tom
>
> --On Wednesday, October 10, 2007 09:47:03 -0400 Adam Fraser
> <adam.n.fraser at gmail.com> wrote:
>
> > 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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> >
> >
> > --
> > 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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> >
>
>
>
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>
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