Extracting energies of different groups

User discussions
1

GROMACS version: 2019.3
GROMACS modification: No

Hi, I’m simulating a system with two different groups, and using temperature annealing. I’m now trying to extract energies of the different groups over the trajectory and have been looking into some of the discussions in this forum to try and figure out how to do this.

I’m running the simulations on a GPU-enabled system, so I can’t use energygrps in the mdp file, otherwise it will revert to CPU only and really slow down the simulation. I saw that I should be able to do mdrun -rerun of the trajectory using a tpr file with energygrps specified in it, however when I tried to do this I got an error saying that temperature annealing is not allowed with rerun.

What I can do to extract the energies of the different groups over the trajectory efficiently please?

Thanks,

Robert

2

You can probably do rerun with a tpr where the annealing has been turned off.

But note that interactionenergies, which are enthalpies, are meaningless in most cases. Most phenomena of interest are driven by free-energy which includes entropy.

3

I’m mostly interested in extracting the temperatures, total Potential, LJ and Coulomb potential of the different groups individually and paired.