[gmx-users] parameters for increased repulsion
spoel at xray.bmc.uu.se
Thu Aug 29 19:16:16 CEST 2002
On Thu, 2002-08-29 at 18:03, Giorgos Karvounis wrote:
> i am trying to set the force field parameters to reproduce a
> L-enkephalin simulation (David van der Spoel et al 1996).
> First of all, it is mentioned that explicit hydrogens are used for the
> polar and aromatic parts but not for the aliphatic. I would imagine that
> using ffgmx2 will do the trick.
> Secondly (and most important) , in order to achieve increased repulsion
> between water oxygen and carbon, i need a parameter set referred as SW
> by Daura et al , 1996.
Normal GROMACS FF includes those aromatic hydrogens (as you can see in
the topology and/or conf.gro file) and also the incerased repulsion. The
GROMOMS96 force field in combination with the recent DMSO model should
also be fine. Just select either 0 or 2 (recommended) for the force
> Because i am an inexperienced user, do i have to change those non-bonded
> interaction parameters myself, or are they somehow implemented?
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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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