[gmx-users] using different force fields
spoel at xray.bmc.uu.se
Wed Aug 21 20:11:59 CEST 2002
On Wed, 2002-08-21 at 19:58, Michael Tallhamer wrote:
> Dear GROMACS Users,
> I am fairly new to GROMACS and would like to use the ffgmx2 force field for
> the system I am working with as to maintain the hydrogens in my system as
> separate atoms and not part of a composite atom as in the ffgmx force field.
> However I am having a hard time getting GROMACS to read from the ffgmx2
> files. I haven't found any reference to this problem in the documentation
> and would appreciate any help those of you who are more experienced than
> myself can provide. Thank you in advance for any information you can offer.
The ffgmx2 ff is useful only for NMR refinement, as the Hs do not carry
a charge (apart from polar Hs) or VanderWaals interaction.
If you want a real all-atom force field you have to use OPLS (preferbly
with TIP4P water).
You can also run the normal GROMOS96 force field, and add the Hs to your
topology afterwards (using the protonate program), if you just want the
Hs for analysis.
> Michael Tallhamer
> Undergraduate Reseacher
> Cleveland State University
> e-mail: tallhamer at hotmail.com
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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://zorn.bmc.uu.se/~spoel
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