[gmx-users] mdrun -rerun problems

George Abadir georgea at ece.ubc.ca
Wed Jul 18 07:07:37 CEST 2007

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,
George B. Abadir

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