[gmx-users] System equilibrium problems

[Parker de Waal]

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

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

Any input would be greatly appreciated!
Parker