[gmx-users] Interaction energy

[Justin A. Lemkul]

Steven Neumann wrote:
> 
> 
> On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Steven Neumann wrote:
> 
> 
> 
>         On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Steven Neumann wrote:
> 
>                Dear Gmx Users,
>                 I would like to calculate the interaction energy (LJ and
>                electrostatic) between each residue and my ligands (10
>         ligands
>                in the system). I would like to see what is the
>         contribution of
>                electrostatic and vdW interactions between ligand and
>         each of my
>                residue. I thought to use g_energy and specify each of my
>                residues in index files but it is not possible. Will you
>         suggest
>                how to do this?
>                
> 
>            For such information, you have to specify these groups as
>         energygrps
>            in the .mdp file.  You can rerun the trajectory using mdrun
>         -rerun
>            and a new .tpr file specifying these groups, but depending on the
>            output frequency, the result may not be as accurate as you'd
>         like.
> 
>            -Justin
> 
>          Thank you Justin. Now I have two groups sepcified in my mdp file:
>          energygrps = Protein LIG
> 
>         How can I specify each residue of my protein separately and each
>         ligand? In my md.gro file I have residues:
> 
>            91GLY 92TYR ..... 161LIG 162LIG...
> 
>          Will it be correct like this
>          energygrps = 91GLY 92 TYR ... 161LIG 162LIG...
>          
> 
> 
>     No.  The names must correspond to valid groups in an index file.
> 
>  
> So do you mean that that I should add my index file with
>  
> 
> grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr
> 
>  
> 
> with specified groups in md.mdp file like they are specified in index 
> file? :) Then just to
> 
>  
> 
> mdrun -rerun -deffnm md2
> 
>  
> 
> Please, let me know whether I am correct or not.
> 

Yes.

-Justin

>  
> 
> Steven
> 
> 
>         If yes, will this simulation take longer? Thank you
> 
> 
>     Perhaps, but certainly your energy file will be considerably larger.
> 
>     -Justin
> 
>          Steven
> 
>          
>          
> 
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================