[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
> parameter.
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.

> Thanks
> SUN,Jian

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

More information about the gromacs.org_gmx-users mailing list