[gmx-users] energy minimisation error

[Justin Lemkul]

On 12/2/19 10:06 AM, Ayesha Fatima wrote:
> Dear All,
> Good morning. I am doing  the Protein Ligand complex simulation tutorial
> from the Gromacs website. I followed the tutorial without any issue. When I
> want to run the energy minimisation md, i get the error message

Are you working through the tutorial, or are you trying to apply its 
method to a different system? There is a big difference.

> Fatal error:
> grid cell cx -2147483648 cy -2147483648 out of range (max 24 24)
> atom -nan -nan -nan, grid->c0 0.000000 0.000000
>
> I suppose the system is blowing up.
>
> There is another error in the nohup file
>
> WARNING: Listed nonbonded interaction between particles 2615 and 2632
> at distance 3.841 which is larger than the table limit 2.470 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
> Not sure which parameter to change
>
> How to resolve the error?

Either you have a bad initial contact that cannot be resolved or your 
ligand topology has inadequate parameters that lead to physical 
instability. Please consult 
http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system, 
which explicitly describes troubleshooting in protein-ligand complexes.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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