[gmx-users] Selecting specific atoms to find average energy of

[XAvier Periole]

On Jun 12, 2010, at 3:10 AM, Justin A. Lemkul wrote:

> Quoting Jennifer Casey <jrcasey20 at gmail.com>:
>
>> Hello,
>>
>> I ran an md simulation, and I have graphed the total average energy  
>> of the
>> system by using g_energy to convert my binary .edr file into a text  
>> based
>> file.  What I want to do is to find the average energy between the  
>> solvent
>> molecules, excluding the energy between the solute-solvent  
>> molecules and the
>> solute-solute molecules.  I was unable to find a way to have  
>> g_energy give
>> me the energy between a specific group.  Is it possible to do  
>> this?  Or do I
>> need to rerun the simulation, and include something like energy  
>> monitor
>> groups?  There is probably a simple command for this that I am  
>> missing (or
>> at least I hope there is).  I would prefer not to have to rerun all  
>> of my md
>> simulations.
>>
>
> You will have to rerun your simulations using a new .tpr file with  
> the desired
> energygrps defined.  The good news is that you simply have to rerun  
> the
> trajectory using mdrun -rerun, which is substantially faster than  
> recalculating
> the whole thing from scratch.
Some complement:
- you have to rerun the trr trajectory file to access hight precision  
coordinates
of your system.
- you'll have to change the update the neighbor list every step  
(nstlist=1).

If not your energies won't be accurate.
>
> -Justin
>
>> Thanks in advance,
>> Jennifer
>>
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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