[gmx-users] what does it mean by 'started mdrun on node 0'
tsjerkw at gmail.com
Thu Nov 29 09:26:49 CET 2012
Hi Yihua Zhou,
Step Time Lambda
> 0 0.00000 0.00000
> Energies (kJ/mol)
> Bond G96Angle Proper Dih. LJ (SR) Coulomb (SR)
> 4.19801e+05 1.40206e+03 3.49599e+03 8.36580e+20 8.17307e+04
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> 8.36580e+20 inf inf inf inf
This is the relevant information from your log file. As you can see there
are several terms at infinite. That indicates there's a problem. The
short-range Lennard-Jones is quite high. Probably you have overlaps in your
system. Did you check the system before running, also making sure that the
PBC are set correctly and not cause overlaps?
Tsjerk A. Wassenaar, Ph.D.
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
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