[gmx-users] tables/user specified potential does not work here
mic0404 at yahoo.com
Thu Dec 11 00:38:00 CET 2003
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
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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