[gmx-users] Need some help with membrane simulation

Ali Khan akk5r at virginia.edu
Thu Jun 5 20:21:07 CEST 2014

Hi all,

I don't know if anyone has experienced this problem before, but I figure I
ask. I have several times run a simulation on a 135A x 135A POPC membrane
acquired fro the charmm-gui website. I wanted now to simulate one that was
slightly larger (150A x 150A). I made the larger membrane on charmm-gui,
and I did everything the same way as I did before (even used the same .mdp
files). After energy minimization, I get an error during my temperature
equilibration as follows:

*Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.4#*
*Wrote pdb files with previous and current coordinates*

*WARNING: Listed nonbonded interaction between particles 31617 and 31619*
*at distance 3f which is larger than the table limit 3f nm.*

*This is likely either a 1,4 interaction, or a listed interaction inside*
*a smaller molecule you are decoupling during a free energy calculation.*
*Since interactions at distances beyond the table cannot be computed,*
*they are skipped until they are inside the table limit again. You will*
*only see this message once, even if it occurs for several interactions.*

*IMPORTANT: This should not happen in a stable simulation, so there is*
*probably something wrong with your system. Only change the table-extension*
*distance in the mdp file if you are really sure that is the reason.*

*Program mdrun, VERSION 4.6.5*
*Source code file: /home/ali/Downloads/gromacs-4.6.5/src/mdlib/pme.c, line:

*Fatal error:*
*5 particles communicated to PME node 1 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.*
*For more information and tips for troubleshooting, please check the
*website at http://www.gromacs.org/Documentation/Errors

I referred to the gromacs website, and it stated that this error means that
my system is blowing up. I have tried several things to fix it (including:
remaking the system on charmm-gui, running energy minimization with small
energy steps [emstep = 0.01, 0.001, 0.0001], energy minimizing to Fmax of
100 kJ kJ/mol/nm instead of 1000, and I have done all these combinations in
both single and double precision) and none of these methods worked. I also
should add that sometimes I am able to perform the temperature
equilibration, but then I would get the same error during the pressure
equilibration. I doubt it is charmm-gui, because they are usually very
reliable in generating membranes.

Does anyone have any suggestions? I can post any of my input files if

Best Wishes,

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