[gmx-users] Unphysical minimization results inconsistent within simulation

[Kimberly Bowal]

Hello,

When minimizing a cluster of simple aromatic molecules, GROMACS will run
but gives me unphysical results (some molecules are crumpled into a ball
and the energies are NaN).  I have gone through the topology file and can't
find an issue, and when I use the same topology file with a different
geometry file of a cluster of the same molecules (generated in a different
way), I have no issues.  I know this issue often is due to atomic overlap,
but I can't see this at all in my system.

I believe this problem is my .gro input file, which I am getting from a
Monte Carlo program, but I can't understand why it would cause an issue.
One thing in particular that confuses me is that within the same cluster of
molecules (.gro file from MC program), some of the molecules are fine and
others are messed up.
To illustrate, here are snapshots of two molecules in the cluster (others
not shown) before the minimisation: https://photos.app.goo.gl/
AHcV4qagnSurbDT12
and the same two molecules after minimisation: https://photos.
app.goo.gl/91sLieiUuUB1SHkm1

I'm happy to include the contents of any input files if that would be
helpful - please let me know.

Thank you very much for your help,
Kimberly