Dear Users, I have a question about separating a system into energy groups. In my system, I have a metal atom and a few residues close to the metal atom (catalytic center). I ran the simulation with out any restraints. In the most representative structure, the catalytic center is completely distorted. To keep the catalytic center as such I am trying to freeze a few of the atoms. For this, I created an index file with the required atoms to freeze and did added the following lines to my .mdp file:
energygrps_excl = Test Test Test SOL freezegrps = Test freezedim = Y Y Y (Test is the name of the group of atoms for which I made the index file and these are the atoms I am freezing) my .mdp file also contains the following line: energygrps = Protein, Na, SOL Now, my question is: The atoms which I defined in the energygrps_excl are present both in the excluding group as well as in the energygrps. So under which group they are exactly considered. With these, I made the tpr file with the follwing command and the simulation is running (though I didnt checked whether the freezed atom positions are fixed or not): grompp -f .mdp -c .pdb -p .top -n .ndx -o .tpr Ram.
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