Energy calculations of residues is zero

User discussions
1

GROMACS version: 2020
GROMACS modification: Yes

Dear Gromacs-Users,
I rerun a trajectory to extract the SR interaction energies of two residues. The output energy from gmx energy is 0 over the course of the whole simulation which is impossible (from visual inspection those residues are too close for 0 interaction). This question is related to an earlier question I posted (thread), but I think I wasn’t specific enough here.

I used a simple index file where the indices of the all residues are defined and added those energy group names to the energygroups input flag of the input .mdp file.
I did not use GPUs to rerun the trajectories and extract the interaction energies! I don’t know why this info still appears…

The partial output of mdrun:

GROMACS: gmx mdrun, version 2020.6
Executable: /home/f/f_kell07/software/gromacs_analysis-2020.6/bin/gmx
Data prefix: /home/f/f_kell07/software/gromacs_analysis-2020.6
Working dir: /scratch/tmp/f_kell07/analysis_mclattice/test_energy_gmx_version/resid1_wat/2020
Command line:
gmx mdrun -v -ntomp 8 -ntmpi 1 -deffnm energycalc_2020 -rerun …/…/dppc_330_fragment.xtc

Reading file energycalc_2020.tpr, VERSION 2020.6 (single precision)
Multiple energy groups is not implemented for GPUs, falling back to the CPU. For better performance, run on the GPU without energy groups and then do gmx mdrun -rerun option on the trajectory with an energy group .tpr file.
Changing nstlist from 20 to 100, rlist from 1.2 to 1.318
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 8 OpenMP threads

Thanks for your efforts to help! :-)
Best
Fabian

2

I’m seeing the same thing when I try and calculate interaction energies for a subset of water molecules. “gmx hbonds” works fine , but “gmx energy -rerun -nb cpu” gives all zeros. The same problem occurs with gromacs 2021.2 and 2022. This is the second thread I’ve found that seems to relate to the problem, but I don’t see any resolution.