[gmx-users] topology defaults directive

David L. Bostick dbostick at physics.unc.edu
Mon Oct 18 20:06:42 CEST 2004

Hi Berk,

I tried setting maxwarn to some large number and then gmxdumped the tpr
file to check the 1-4 interactions a while back.  If I remember correctly,
the LJ14 pairs looked as though they were generated with fudgeLJ, and not
taken from the pairtypes list... although I could be mistaken.. I'll check
again.  The only sure way I found to get the dumped tpr file to look proper
was to explicitly place the interaction under the pairs directive in the
molecule.itp file.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Mon, 18 Oct 2004, Berk Hess wrote:

> >I tried using gen-pairs=yes and generating a pairtypes list for certain 1-4
> >LJ interactions in a molecule.itp file. I listed the pairtypes directly
> >below the atomtypes section.  However, grompp complained about
> >all of the pairtypes in the list, giving
> >
> >WARNING 1 [file "ffoplsaa_lipidnb.itp", line 737]:
> >   Trying to add LJ-14 while the default nonbond type is LJ (SR)
> >WARNING 2 [file "ffoplsaa_lipidnb.itp", line 738]:
> >   Trying to add LJ-14 while the default nonbond type is LJ (SR)
> >etc.
> >etc.
> >
> >Perhaps this means that the only choice is to list the interactions under
> >the pairs section?
> You should ignore these warnings (use the -maxwarn option if there are too
> many).
> I'll remove the warning in the next release.
> You can check the final parameters by using gmxdump -s or gmxcheck -s1 -s2
> on your tpr files.
> Berk.
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