[gmx-users] (no subject)

rsf romelia at caltech.edu
Thu Sep 17 18:56:41 CEST 2009


I have a silly question about the implementation of the Gromos forcefield
in gromacs, particularly about the exclusions. I have the gromos manual
and have seen that, for instance, for the residue MET there are only 1st
and 2nd neighbors exclusions defined for it. However, when I build a
protein using the gromos forcefield in gromacs and print out the
exclusions generated (using gmxdump), I get more than the ones I would get
according to gromos.

I am trying to validate my results by comparing with someone else's run
that was performed using gromos directly and the description of the
molecules don't seem to match in that part. The file dumped from gromos
has only the exclusions defined as in the gromos manual. I assume they
should be equivalent and both codes should give rise to the same
forcefield description but I would greatly appreciate if someone could
comment on this so I can understand better how to compare these two files.

Also, if someone knows how to transform gromacs truncated octahedral
coordinates to a format that can be read by gromos I would really
appreciate it.


Romelia Salomon
Miller Group
132 Noyes
Chemistry Department

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