[gmx-users] problem with NVT equilibration for membrane protein

Justin Lemkul jalemkul at vt.edu
Mon May 12 14:04:38 CEST 2014

On 5/12/14, 5:32 AM, Floriane Montanari wrote:
> Dear all,
> I am working with an homology model of a protein inserted in a POPC membrane.
> I first ran minimization on the system, which ended up with I think
> "reasonable" values for Fmax and Epot:
> Steepest Descents converged to Fmax < 1000 in 1390 steps
> Potential Energy  = -1.2822042e+06
> Maximum force     =  8.4696790e+02 on atom 7447
> Norm of force     =  2.2902491e+01
> I am using the Amber99sb forcefield modified to include Berger parameters
> for my lipids.
> I am now trying to run NVT using the parameter file sent as attachment. I
> tried to lower the temperature ref_t / different values of cutoffs
> rcoulomb, etc. / a Fourier transform of 0.12 as seen in literature
> but all this only ended up in the same error:
> Depending on how many threads I launch mdrun with, I get
> - either a particles error
> Fatal error:
> 3 particles communicated to PME node 3 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> (more or less particles / more or less nodes depending on the runs)
> - or a segmentation fault
> In any cases, those errors occur right at the end of step 0.
> Is there anything I am doing wrong? Can someone give me advices on how to
> fix this?
> I can send many other files if needed (my topol file, my minimized system,
> my forcefield...).
> I am running gromacs 4.5.3.

Possible culprits:

1. Incorrect modification/implementation of the force field.  Combining Amber 
and Berger seems like a very awkward thing to do, IMHO.

2. Incorrect .mdp settings.  You said above you've played with nonbonded 
cutoffs, which is usually unwise.  Every force field has a set of nonbonded 
cutoff values that should be rigorously adhered to, not toyed with.



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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