[gmx-users] Energygrps

[Ahmed Mashaly]

Hi
What is the default engerygrps to be written if I don't specify them in the mdp file?
And if I have more than one ligand and want to calculate the energy between them and the protein, and also between one part of the protein (loop) and the rest of the protein I should make an index identifying each ligand indvidually and this part too and my energygrps will be protein lig1 protein lig2 protein loop ...
If I don't specify this from the beginning is it the same to get with mdrun rerun or will be different? This questions might have been answered before in archive, but there is a problem to access it, any idea when will it be resolved?
Kind Regards,Ahmed