[gmx-users] force-field parameters

[K.A. Feenstra]

David wrote:
> 
> On Fri, 2002-08-30 at 21:14, David L. Bostick wrote:
> >
> > You can rename the file to something that doesn't exist in the distributed
> > /top directory and in the top of you mdp file specify..
> >
> > include                 = -I$GMXDATA/top -I./
> >
> > although the -I./ is probably unnecessarry because I believe the current
> > directory is already searched when grompp puts together the topology.  If
> > you really want to be sure you use nothing in the /top directory, just dont
> > include it with -I$GMXDATA/top.  I think this is right although please
> > somebody correct me if not.
> The working directory is always searched first. Furthermore you can
> check the topology using gmxdump. Look for idef, and you'll find the
> matrix of LJ parameters written out linearly (i.e. row1, row2, .. rowN)
> so for 20 different atom types you will find 400 LJ parameters.

Also, you can compare your original .tpr file (with the standard parameters)
and your new .tpr file (with hopefully your modified parameters), by
using 'gmxcheck -s1 original.tpr -s2 new.tpr'. It will print any and all
parameter(s) that differ between the files.

-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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