[gmx-users] Need some help with membrane simulation

[Mark Abraham]

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
> >
> > ==================================================
> >
> > --
> > 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-request at 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-request at gromacs.org.
>