Hi,
I got spuriously large distance restraint potential energy when running mdrun
with multiple OpenMP threads and the system adopts a weird configuration sooner
or later (depending on the restraint force constant) while the same simulation
(same tpr file) runs fine. Here are the Dis. Res. related mdp option I used:
disre = simple
disre-weighting = conservative
disre-tau = 0
disre-fc = 1e-5
nstdisreout = 10000
and I tried mdrun using a single MPI rank and giving 1, 2, 4 to -ntomp and only
-ntomp = 1 gave sane results. The log file from the 1 OpenMP thread looks like:
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Angle G96Angle LJ (SR) Coulomb (SR)
2.16662e+01 0.00000e+00 1.96570e+03 9.15548e+03 0.00000e+00
Dis. Rest. D.R.Viol. (nm) Potential Kinetic En. Total Energy
5.56697e+04 2.90805e+04 6.68126e+04 1.57240e+04 8.25365e+04
Temperature Pressure (bar)
2.99970e+02 -6.28303e-07
while that from 2 OpenMP threads looks like:
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Angle G96Angle LJ (SR) Coulomb (SR)
2.16662e+01 0.00000e+00 1.96571e+03 9.15548e+03 0.00000e+00
Dis. Rest. D.R.Viol. (nm) Potential Kinetic En. Total Energy
1.96610e+07 4.12632e+05 1.96722e+07 1.57284e+04 1.96879e+07
Temperature Pressure (bar)
3.00055e+02 5.46943e-06
It looks like all the other potential energy terms are the same independent of
the number of OpenMP threads except for Dis. Rest.. Can anyone tell me if I'm
hitting a bug in GROMACS or if there's something I missed in setting up
distance restraint?
Thanks,
Tim
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