[gmx-users] Questions about energy groups!

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 22 16:15:53 CET 2009

Zhong Zheng wrote:
> Dear all
> I have successfully run though the energy minimization on my target 
> protein. I am trying to extract the backbone-backbone interactions from 
> the energy output files. My understanding is that I need to define the 
> energy groups in the grompp.mdp. This is what I edited:
> energygrps               = mainchain
> I also have the index file ready. "mainchain" is defined in it which is 
> actually a default group.  However I am getting the following error 
> message when I move on to run grompp (grompp -n *.ndx) :
> atoms 1 and 2 in charge group 1 of molecule type 'Protein_L' are in 
> different energy groups
> Atom 1&2 are the N and H1 in an Ala. They are defined in one charge 
> group. If I manually modify the topol file and make them into different 
> charge groups, the program will move on and complain about another two 
> atoms. However, the backbone atoms (N C CA O) ARE put in different 
> charge group in the opls force field I am using.
> So my questions are:
> 1. Can I extract the backbone-backbone interactions directly using 
> g_energy or some other commands?

Once written to the energy file, no, the energy terms cannot be separated.

> 2. How can I fix this error? Do I have to put all the backbone atoms in 
> the same charge group?

You are going to have a problem any time you try to split charge groups between 
energy groups.  MainChain does not include H atoms, thus you are seeing the 
error you describe above.

Ask yourself if it is meaningful to analyze energies of an incomplete group 
(i.e., those that have had bonds to neighboring atoms broken).  To do what you 
are thinking of, you will at least have to use the MainChain+H group, but that 
may fail as well, depending on how the charge groups are set up.


> Many thanks.
> Zhong Zheng
> Ph.D candidate
> Physics Dept., City College-CUNY
> Marshak Science Building J-419 ,
> 160 Convent Ave,
> New York, NY 10031 USA
> Tel: (212)650-6079
> MCCE new wiki:
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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