[gmx-users] electrostatic energy calculation

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Tue Aug 2 12:17:46 CEST 2016

Yes you need to use mdrun with the -rerun option. I did this as follows:

1. use make_ndx to add the desired selections into your index
2. make a new mdp with the energygrps option listing two index items by name
3. grompp -f rerun.mdp -c npt.gro -p topol.top -o rerun.tpr -n index.ndx
4. mdrun -v -deffnm rerun -rerun md.trr
5. gmx energy -f rerun.edr and select the terms corresponding to coulomb
SR and LR

You can use the -sum option of g_energy to sum these terms together.

Best wishes

> Dear all,
> I want to calculate the electrostatic energy (coulomb SR and LR) for a set
> of molecules during the whole simulation. I used g_energy -f ener.edr -o
> (with or without -nmol option), but it only gives me 1 average output for
> the last step.I tried g_enemat -f -etot (-emat) but it stops needing a
> group.dat file. Is there a way to calculate coulomb energy in all steps
> preferably for a set of desired charged molecules?
> Thanks.
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