msnayeem at gmail.com
Mon Feb 7 14:32:03 CET 2011
That means in energy group in .mdp file I should write interface.ndx
and tell me if on interface there is hydrogen bond then its value I
will get or not.
On Mon, Feb 7, 2011 at 6:50 PM, Justin A. Lemkul <jalemkul at 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.
>> 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
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