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

Justin Lemkul jalemkul at vt.edu
Tue Aug 28 16:08:25 CEST 2018

On 8/28/18 10:04 AM, Irem Altan wrote:
> Hi,
> 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.

The contents of index.ndx are irrelevant unless you've actually specific 
which energygrps you want to define (in the .mdp file). Also, why are 
you using -maxwarn 1? This should almost never be done.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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