Hi there, I'm trying to embed a protein with MG and ATP into the membrane. Based on the index file with *protein_MG_ATP* as one group and *membrane_Ion_Sol* the other, I listed these two groups as energygrps in Sample.mdp (attached), and the former as freezegrps.
However, this didn't allow me to proceed with "energygrp_excl = protein_MG_ATP protein_MG_ATP" as I kept on getting this error: "Can not exclude the lattice Coulomb energy between energy groups" Tried to remove freeze group or energy exclusion groups altogether but got other errors instead, basically saying that freeze group is required and energy exclusion groups are necessary for energy exclusion in the freeze group. Checked the only relevant thread with answers out there and found that mine is a different issue - the total charge of each group is nonzero. I would really appreciate your help! Ava P.S. Parameters in Sample.mdp were modified semi-arbitrarily, referencing the previous mdout.mdp and the default settings.
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