[gmx-users] rerun confusion

[SebastianWaltz]

Hallo all together,

I am working on a system of a small peptide solvated in CHCl3.
I want to obtain the forces on the peptide atoms  induced by the
solvent. For this I used the rerun option of mdrun_d. I did it now in
two ways:
1st: using trjconv to get the pure peptide trajectory. When using the
rerun option with no special configurations of the .mdp file. If the
obtained force are pair additive I should get the wanted result if I
subtract from the forces of the original trajectory the rerun forces.
2nd: using the original trajectory and changing the options of the .mdp
file as follows:
energygrps          =  Protein SOL
energygrp_excl        =  Protein Protein SOL SOL
and changing the coulomb type to Cut-off because of the separation
problem using PME.

Comparing this two results I realize that they are totally different.
There is no correlation to detect between this two.
I am wondering now which way to go to get the correct answer for my
question. I probably just do not understand the energygrps and
energygrp_excl option right.
Using rerun with the same trajectory and the same .mdp option except
changing PME to Cut-off gives the same result as the original trajectory
or at least up to the last 3 decimal places of a double value.

I would be really happy if someone can help me

Thanks a lot

Sebastian