[gmx-users] Unphysical minimization results inconsistent within simulation

[Justin Lemkul]

On 1/22/18 10:38 AM, Kimberly Bowal wrote:
> Thank you Justin.  Neither my MD or MC simulations are using PBC so I don't
> think atomic overlap is the problem.
>
> To help see this, here are snapshots of the whole molecular cluster before (
> https://photos.app.goo.gl/dDUJ8f2s3MXyfTSw2) and after (
> https://photos.app.goo.gl/tGReLmIYVFD4038s1) minimization. As you can see,
> not all of the molecules are crumpled and crumpled molecules are found
> throughout the cluster.
>
> One thought is that the input molecule geometries from the MC code (which
> are showing the behaviour pictured above) have slightly longer bond lengths
> than the input molecule geometries that are minimised successfully.
> However if that were the issue, why would I see some molecules in the
> cluster affected and others not?

You wouldn't, and "slightly" different bond lengths should be trivial to 
resolve by energy minimization.

Are all molecules identical? How were they parametrized and validated? 
Does a single molecule minimize stably in vacuo? A dimer?

-Justin

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

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