[gmx-users] NVT equilibration

[Shima Arasteh]

Dear gmx users,

I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K. 

Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error:
Fatal error:
1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.


I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally? 


Cheers,
Shima