[gmx-users] Need some help with membrane simulation

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 5 20:37:20 CEST 2014

On Jun 5, 2014 8:24 PM, "Ali Khan" <akk5r at virginia.edu> wrote:
> 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
> *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,
> 851*
> *Fatal error:*
> *5 particles communicated to PME node 1 are more than 2/3 times the
> out of the domain decomposition cell of their charge group in dimension
> *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
> <http://www.gromacs.org/Documentation/Errors>*
> *-------------------------------------------------------*
> I referred to the gromacs website, and it stated that this error means
> 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
> 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
> requested.

.mdp files might be useful, but following the advice at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up is definitely a
good course.


> Best Wishes,
> Ali
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