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? 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?
Thank you very much in advance,
Regards,
George B. Abadir
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