Yes of course I looked at the output but I thought is I specify energy
groups it will output only those specified and not the whole system.
However I tried a short run and it did output both. For the crash it
turned out it is because all the nodes try to read the huge trajectory
file at the same time if this may help somebody in the future. We are
still trying to figure out how to solve this problem anyway.
Thanks for your time.
George
Mark Abraham wrote:
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
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