[gmx-users] mdrun -rerun problems
Mark.Abraham at anu.edu.au
Thu Jul 19 06:40:26 CEST 2007
George Abadir wrote:
> Hi all,
> I am running simulations of carbon nanotubes and amino acids in
> water. I need to calculate the potential energies for the whole system
> as well as the interaction energy between the CNT and amino acid. What
> I am tried to do is to calculate the energy for the whole system first
> (i.e. I did not introduce any energygrps in the run.mdp file) and then
> use the rerun option to calculate the interaction energy after
> introducing "energygrps= CNT Protein SOL" into the run.mdp file.
> However, each time I try to run this second step the cluster on which I
> run the simulation crashes with a message "Kernel panicked"!
> Does any body know about this problem?
Yeah, something's broken that's probably got nothing to do with GROMACS,
or the fact you're doing a re-run.
> Is there another way to get both
> the potential energy of the system as well as the interaction potential
> energy? I understand that if I write "energygrps= CNT Protein SOL" from
> the very beginning the energy of the whole system won't be written, is
> that right?
mdrun always calculates the total potential and kinetic energy, and
outputs it according to nstxxx flags.
Have you not looked at typical output, or typical .edr file contents?
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