Steven Neumann wrote:
On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
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