[gmx-users] energy groups

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 17 12:42:38 CEST 2008

rams rams wrote:
> 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.

A note of etiquette - don't double post; it makes you look impatient.  Everyone 
here has important work they're doing, too, you know :-)

That said, if you don't know what you're doing, don't do it until you do :-)

What you've done is exclude nonbonded interactions within the atoms of the 
"Test" group (with respect to themselves), and between "Test" and the solvent. 
Interactions between "Test" and the rest of the protein, Na+, etc. are still 
included in the calculations.

Wouldn't it be simpler to just use position restraints?  Or investigate why your 
catalytic center is so distorted?  Maybe there is a larger problem with whatever 
you've done...


> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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