[gmx-users] Gromacs4: minimization hangs

[Lillian Chong]

I ran the following for the minimization using mpich2:
mpiexec -n 8 mdrun_mpi -s min.tpr -c min.gro -o min.trr -g min.log -e min.edr

On Fri, Oct 17, 2008 at 12:36 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> Lillian Chong wrote:
>>
>> Dear Gromacs Users,
>>
>> When I run a steepest descent minimization with the parallel version
>> of mdrun in Gromacs 4, it runs to completion (all 1000 steps), but
>> does not exit.  See below for the tail end of the log file (notice
>> there are not timings and the usual Gromacs quote at the end).  The
>> serial version of the Gromacs 4 mdrun runs this minimization fine and
>> exits as it should.  I did not have this issue with the Gromacs4rc3
>> parallel mdrun.  Do you know what might be going wrong?
>
> Which mpi version are you using?
>>
>> I've attached the min.mdp and min.tpr files.
>>
>> Best regards,
>> Lillian
>> ====================
>> Tail end of log file:
>>          Step           Time         Lambda
>>          1000     1000.00000        0.00000
>>
>>  Energies (kJ/mol)
>>          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
>>   2.75995e+01    1.01358e+02    5.12660e+00    1.82811e+02    2.18810e+02
>>    Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>>   8.24670e+02    1.97157e+04   -9.79168e+02   -1.44989e+05   -1.75892e+04
>>     Potential Pressure (bar)
>>  -1.42482e+05    1.42736e+04
>>
>>
>> ------------------------------------------------------------------------
>>
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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-- 
Lillian T. Chong
Assistant Professor
Department of Chemistry
University of Pittsburgh
219 Parkman Avenue
Pittsburgh, PA 15260
(412) 624-6026