[gmx-users] rerun doesn't calculate Coulomb & LJ interactions between groups

Irem Altan ia41 at duke.edu
Tue Aug 28 16:04:40 CEST 2018


I ran some umbrella sampling simulations on GPUs. I want to get the Coulomb and LJ energy between certain groups (chain A - chain B, chain A - solvent, etc.) , so I ran rerun:
gmx mdrun -rerun umbrella1.xtc -nb cpu -v -deffnm umbrella1
However, when I run gmx energy on the output .edr file:
gmx energy -f umbrella1.edr -o umbrella1_ener.xvg
I only get 50 terms listed, as opposed to ~90 that contains things like "LJ-SR:SOL-Chain_A". What am I missing?
The executable is created with the following command:
gmx grompp -f umbrella.mdp -c conf1.gro -p topol.top -n index.ndx -maxwarn 1 -o umbrella1.tpr
where chain A, chain B, and SOL are defined in index.ndx.

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