shahid nayeem wrote:
That means in energy group in .mdp file I should write interface.ndx
No, you specify the names of the desired groups using the energygrps keyword,
not the name of the .ndx file. You pass the .ndx file to grompp.
and tell me if on interface there is hydrogen bond then its value I
will get or not.
The energygrps feature has nothing to do with hydrogen bonds. You analyze those
with g_hbond.
-Justin
Shahid Nayeem
On Mon, Feb 7, 2011 at 6:50 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
shahid nayeem wrote:
Dear User
I am doing MD on protein complex keeping backbone as well as side
chain of all residues which is not on th interface fixed. For this I
prepared posre_backbone_sidechain.itp and defined this in .top file
for full MD. Now I want to know from the trajectory the best side
chain conformation of the interface residues for which I want to see
the change in total energy of the interface residues throught the
trajectory. I prepared index file for interface residues. But g_energy
command does not takes -n index.ndx to calculate energy of these
groups. How can I do that. Please suggest.
You can set energygrps in the .mdp file and use mdrun -rerun to re-calculate
the components of the nonbonded interaction energy between different groups.
You cannot decompose the total energy or bonded terms. If you've used PME,
the long-range term cannot be decomposed, either.
-Justin
Thanking you
Shahid Nayeem
--
========================================
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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========================================
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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