[gmx-users] Energy-groups?

[nishap.patel at utoronto.ca]

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.


>
>
> 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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