[gmx-users] Two ligands - One CPU ?
jalemkul at vt.edu
Tue Feb 21 15:23:01 CET 2017
On 2/21/17 6:27 AM, Julian wrote:
> Hello James,
> Thanks for the information! Here is the link
Your mdrun command doesn't specify how many threads you want:
gmx mdrun -c sting_c2e_nvt.pdb -deffnm sting_c2e_nvt -nice 19
so mdrun tries to use everything it can find:
Using 1 MPI thread
Using 8 OpenMP threads
But you have a much bigger problem in that the initial state of your system is
Initial temperature: 27154 K
Started mdrun on rank 0 Mon Feb 20 13:18:21 2017
Step Time Lambda
0 0.00000 0.00000
Large VCM(group rest): 93.05952, 680.99396, -32.68222, Temp-cm:
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
2.26179e+04 1.78402e+04 6.42050e+01 1.53991e+04 4.39054e+04
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest.
1.46511e+15 -6.16254e+03 -6.92922e+05 4.29973e+04 4.10620e+03
Potential Kinetic En. Total Energy Conserved En. Temperature
1.46511e+15 1.11383e+30 1.11383e+30 1.11383e+30 3.04790e+27
Pres. DC (bar) Pressure (bar) Constr. rmsd
-2.30244e+02 2.77096e+28 4.91514e+11
> Best wishes,
> On 21 February 2017 at 11:54, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>> Hi Julian,
>> You can't send attachments to this list. Please upload the log file
>> somewhere and provide a link.
>> Best wishes
>>> Dear Gromacs Users,
>>> I have a very strange problem that I have not seen before: I am running
>>> three simulations of three crystal structures. It is the same protein
>>> to different ligands - in one case the ligand is two times present in the
>>> protein. All preparation steps and commands were exactly the same.
>>> When running the md simulation, strangely the protein with the two
>>> is running only on one CPU while the other two simulations run on several
>>> CPUs. Has anybody experienced something like this before?
>>> I am also attaching the log file but I didn't see anything that looked
>>> suspicious to me.
>>> Thank you for your answers.
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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