[gmx-users] Need some help with membrane simulation

[Ali Khan]

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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