[gmx-users] Re: Something wrong with the force field parameter
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 20 10:44:20 CEST 2006
SUN, Jian wrote:
> Dear all,
> I am now running the MD simulation for a small molecular not covered
> by the rtp file. The force field I used is oplsaa.
> I genereated the gro and top file using PRODRG program (from its
> website). and added them to the ffoplsaa.rtp ffoplsaa.hdb. Finally I
> got the gro and top file for my small molecular. But when I run the
> energy minimization for this molecular, the atoms detached and run out
> of the bond range. There must be something wrong with the force field
This points more to errors in the topology, i.e. missing bonds.
> Would you kindly show me, how to generate the force field parameter
> for the oplsaa?
Please read Jorgensen's papers.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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