[gmx-users] equilibration error

Stephani Macalino stephanimacalino at gmail.com
Thu Oct 11 07:16:24 CEST 2018

I am planing to do MD of a membrane protein bound to a ligand.
I already have my files and I am doing my 6 step equilibration with
reducing force constants.
However, in the 5th step, it gave an error saying that the previous system
(4th step) was not well equilibrated:

Fatal error:
5 particles communicated to PME rank 0 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

I'm a newbie to this and don't completely understand the error.
Since it says the previous system is not well equilibrated, should I
increase the steps for equilibration?

I am wary to change the force constant values since I did 100ns MD for apo
WT and mutant structures for the same protein that I am now doing with the

Hope you can suggest some ways to solve this problem. Thanks in advance!


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