[gmx-users] Energy-groups?

[nishap.patel at utoronto.ca]

I see. It did work . Thanks a lot Justin!

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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
>
> ========================================
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