[gmx-users] Gromacs 5.0.1 restart simulation

[wh]

Dear Gromacs Users,

 

Recently when I tried to restart a md simulation from previous one using
convert-tpr with version 5.0.1 , the task failed giving the error message:

 

X particles communicated to PME node Y are more than a cell length out of
the domain decomposition cell of their charge group

 

I tried several way to solve it, including modify the equilibration setting
as it said in the gromacs error page, and all failed. If I just run one
simulation for a long time, it will not crash, at least can do further than
the time point it crashed when using restart.

Does anyone have any idea why this happen and how to solve it?  I used the
syntax:

gmx convert-tpr -s input.tpr -f input.trr -e input.edr -o output.tpr -extend
10000

Any suggestion will be greatly appreciated