[gmx-users] mdrun -rerun problems

Mark Abraham 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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