[gmx-users] mdrun -rerun problems

[Mark Abraham]

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?

Mark