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
--
==================================================
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.
