[gmx-users] mdrun -rerun to obtain the non-bond interaction energy among energy groups

Dai Ling (IHPC) dail at ihpc.a-star.edu.sg
Wed Apr 6 07:03:31 CEST 2016

Dear gmx-user:

I want to plot the non-bond interaction energy between energy-groups. With reading from the history of this mailing-list, I need to use "rerun" to obtain these values. Since I have set all the energy groups in .mdp file initially. So that, after the first mdrun, I just use the same .mdp file, index file  to grompp the a new (but is the same) .tpr file, then rerun it with
gmx mdrun -f xx.tpr -rerun xx.xtc (the trajectory from first mdrun)

however, based on the newly ouput ener.edr file, when I check with "gmx energy -f ener.edr", the LJ energy for individual groups is still zero. And in worsen, the total system energy changed to "nan" after rerun (which is correct after first run).

As I am still new to gromacs, would be highly appreciated for any suggestions.

Thanks & Rgds!
Dai Ling

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