[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

>> 

 

>Do not supply .trr and .edr files; just increase the number of steps and
continue from the existing checkpoint with mdrun -cpi.  What you're doing is
based on ancient syntax that is no longer relevant.  I'm guessing that
you're probably winding up with discontinuous states somehow.

 

>http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_
4_and_Newer

 

>-Justin

 

Thank you so much for your timely reply, yet I tried mdrun -s input.tpr -cpi
input.cpt -append

It still gave the same error message. Could it be a bug? Or I did something
wrong?