Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 7 14:33:36 CET 2011
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
> Shahid Nayeem
> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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