[gmx-users] Energy-groups?

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
> Thanks Justin! I do want the non-bonded potential between my solute and 
> solvent. So in my .mdp file I put my solute and solvent as energygrps 
> and ran mdrun using this command:
>   mdrun -s md1.tpr(including energygrps) -rerun md.xtc (my trajectory)
> 
> Is that correct? I don't understand how it would be faster or any 
> different from running the simulation from scratch, because in my .mdp 
> file it still has time of 100ns. I just modified the energygrps.
> 

It should be significantly faster.  In this case, mdrun is not doing the 
integration, it's simply using the known positions to re-calculate energies.

-Justin

> 
>>
>>
>> nishap.patel at utoronto.ca wrote:
>>> Hello,
>>>
>>>   I want to plot the interaction potential energy between my solute 
>>>  and solvent. In my .mdp file I did not mention anything under  
>>> energygrps,so I am thinking it calculates the energies for the  whole 
>>> system. But is there a way I can extract say for example  LJ-14 term 
>>> between my solute and solvent using the same .edr file?  Or would I 
>>> have to specify my energygrps and run the simulation  again.
>>>
>>
>> 1-4 interactions are intramolecular, so there should be no
>> solute-solvent 1-4 term.  If you want nonbonded potentials decomposed,
>> yes, you have to rerun your trajectory (mdrun -rerun, not from scratch)
>> with a .tpr file specifying the desired groups.
>>
>> -Justin
>>
>>> Thanks.
>>>
>>> Nisha
>>>
>>
>> -- 
>> ========================================
>>
>> 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

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