[gmx-users] Unphysical minimization results inconsistent within simulation

[Justin Lemkul]

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 
trashed.

-Justin

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

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