[gmx-users] tables/user specified potential does not work here
spoel at xray.bmc.uu.se
Thu Dec 11 08:29:01 CET 2003
On Thu, 2003-12-11 at 00:36, m b wrote:
> 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)?
the whole potential
> - what are the signs of each term supposed to be ?
for coulomb related:
1/x and 2/x^3
both positive, this will be multiplied by the product of the charges
obviously. Please take into account the right units (nm, kJ/mol, 1/4 pi
eps0) etc. Compare your potential to one of the files present in
> - 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 ?
No, but you should go at least 1 nm beyond the cut-off in your tables.
> 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 ?
Hm, that is weird. Please check the energies at the first step. You may
have to turn off constraints. You are not combining the table with an
epsilon_RF that is not 1?
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David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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