[gmx-users] System equilibrium problems

[Mark Abraham]

On Thu, Jun 13, 2013 at 11:59 PM, Parker de Waal
<Parker.deWaal09 at kzoo.edu>wrote:

> Hi everyone,
>
> I recently tried to perform an 25 ns simulation on 12 nodes and was greeted
> with this error around 3.2 ns into the run.
>
> '3 particles communicated to PME node 9 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.'
>
> To my knowledge the system has reached equilibrium as shown by energy
> minimization, nvt and npt runs prior to the md run. The only thing that
> concerns me is the Pressure average of 1.9
>

This is normal, see
http://www.gromacs.org/Documentation/Terminology/Pressure


>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Potential                   -921529      32000    94074.9    -214425
>  (kJ/mol)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Temperature                 300.033       0.16    1.57434  -0.790469  (K)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Pressure                    1.94649       0.32    91.4545    1.28586  (bar)
> Density                     1012.96      0.037   0.778484 -0.0126246
>  (kg/m^3)
>
> Additionally here is a link to my md.mdp file
> https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh


Seems fine, apart from fourierspacing being rather more lax than normal. Be
sure your settings are compatible with those used for your force field.

Mark


>
>
> Any input would be greatly appreciated!
> Parker
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