[gmx-users] what does it mean by 'started mdrun on node 0'

Tsjerk Wassenaar 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.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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