Justin, I have tried both manually fixed the offending atoms (by slightly changing the z coordinates of the offending atoms in the .gro file) than running energy minimization, and letting a double precision energy minimization to minimize the forces on the system. The force will always drop below 1000 kj/mol/nm, but I still get the error during temperature equilibration.
On Thu, Jun 5, 2014 at 2:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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 >> GROMACS* >> *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 consequences. > > -Justin > > -- > ================================================== > > 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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.