[gmx-users] octane slab help
David van der Spoel
spoel at xray.bmc.uu.se
Fri Nov 29 10:14:29 CET 2002
On Fri, 2002-11-29 at 09:59, J Simms wrote:
> Hi all,
> I am thinking about making an octane slab for protein, hydrophobic
> simulations. Can I just get the PDB & .itp file from PRODRG, and
> go from there or is there special considerations to take into
> account?? Ie Gromos96 parameters for small hydrocarbons.
> As usual ANY help would be emotionally accepted.
> John ;-)
check the gmx/share/top directory. There is a topology for decane that
you can adapt for octane (and coordinates too, look for dec*). Take care
with those flammable liquids.
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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