[gmx-users] Chloride parameters in ffgmx
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 30 13:06:01 CEST 2003
On Wed, 2003-04-30 at 12:53, hugo verli wrote:
> Hi, David,
> the topology goes in attachment.
> I did not setup exclusions in .top file. Could this be the reason for my results?
It seems that your force constants for the bonds correspond to the
GROMOS96 bonding potential, while you select the harmonic bond (fu=1 iso
2). If you use constraints this is not a problem, otherwise it could
generate strange frequencies.
So, if you use constraints it should work, otherwise it might be wrong.
> > > Yes,
> > >
> > > the geometry of chloroform moleculas is ok, as well as the box.
> > >
> > Can you send the topology anyway? Are the excluisions OK?
> > --
> > Groeten, David.
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
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://xray.bmc.uu.se/~spoel
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