[gmx-users] tables/user specified potential does not work here

m b mic0404 at yahoo.com
Thu Dec 11 00:38:00 CET 2003

dear gmx-users,

I just tried out the table feature implemented in
Gromacs (3.1.4) to use a modified electrostic 
potential (generalized reaction field from
Hummer/Neumann). The attempt failed miserably.

I have a rather simple system (a short polymer
upon a frozen graphite surface) which is perfectly
well-behaved when I use the normal force-routines 
(both cutoff and PME). 

When I use a pre-calculated table, however,
with the very same starting configuration,
topology and the same md.mdp file (except for the
"coulombtype = User" directive) the system
blows up at step zero with HUGE LINCS
deviations. (not even energy minimisation

At first I thought the problem might be
my self-made table.xvg file, since the
documentation is all but clear about
its contents ...
- should it include the WHOLE
potential -1/x*s(x) and its second derivative
or only the scaling factors s(x) and s''(x)?
- what are the signs of each term supposed to be ?
- does it make a difference what values I choose for
those terms that are actually not used at all (the VdW
terms in my case) and also the values beyond the
cutoff ?

Be that as it may, it does not seem to be the
problem (though I would appreciate somebody
answering the above questions!)
because the system also blows up when I use 
the table6-12.xvg file that comes with Gromacs.

any ideas ?

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