[gmx-users] Need some help with membrane simulation

Justin Lemkul jalemkul at vt.edu
Thu Jun 5 20:37:44 CEST 2014

On 6/5/14, 2:11 PM, Ali Khan 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 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:
> 851*
> *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
> <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.

On the contrary, we've had numerous reports of crashing membranes, due to some 
clashes in the starting structures.  Manual modifications to the coordinates of 
the offending atoms (fractions of an Angstrom, really) usually solves it.  The 
output of EM tells you where the maximum force is.  How big is this force?  What 
atom is it acting upon?  That's where you start your investigation.

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

Always post an .mdp file when a run is crashing.  Membranes can be particularly 
challenging to get right; small errors in settings can have catastrophic 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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