[gmx-users] Unphysical minimization results inconsistent within simulation

Justin Lemkul jalemkul at vt.edu
Mon Jan 22 13:55:39 CET 2018

On 1/22/18 4:41 AM, Kimberly Bowal wrote:
> 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.

Are molecules overlapping via PBC? Is your MC code PBC-aware? The 
example you showed appears to manifest large displacements of both 
molecules, suggesting that you may be using a very small box and the 
molecules are actually overlapping, so one is fine and the other gets 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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