[gmx-users] energy groups

rams rams rams.crux at gmail.com
Thu Jul 17 04:29:06 CEST 2008

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

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