[gmx-users] Need some help with membrane simulation

Thu Jun 5 22:16:43 CEST 2014

I tried that as well. I have done the nvt with 2 fs, 1 fs, and 0.5 fs time
step, and I get the same error.

On Thu, Jun 5, 2014 at 4:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> So maybe try not using a time step suitable for an equilibrated system when
> you know your system is not close! :-)
>
> Mark
>
>
> On Thu, Jun 5, 2014 at 8:52 PM, Ali Khan <akk5r at virginia.edu> wrote:
>
> > 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 <jalemkul at 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
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
> > >
> > > --
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