[gmx-users] Two ligands - One CPU ?

[Justin Lemkul]

On 2/21/17 6:27 AM, Julian wrote:
> Hello James,
>
> Thanks for the information! Here is the link
> <https://drive.google.com/file/d/0B2M9aqeJrxnYLVZXLWk5NktDZGM/view?usp=sharing>
>

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 
wildly unphysical:

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: 
1.13021e+07
    Energies (kJ/mol)
           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

-Justin

> Best wishes,
> Julian
>
> 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
>> James
>>
>>> 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
>>> bound
>>> 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
>> ligands
>>> 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.
>>> Julian
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>>
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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
http://mackerell.umaryland.edu/~jalemkul

==================================================