[gmx-users] "energygrps" option for separating Bonded interactions

[Debdas Dhabal]

Dear Justin,

Thanks a lot for your kind help. Yes, these don't mean anything
quantitatively.  I Just wanted to have a qualitative comparison between the
two states.

With regards
 Debdas

On Fri, May 18, 2018 at 4:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/18/18 4:01 PM, Debdas Dhabal wrote:
>
>> Dear all,
>>
>> I wonder if GROMACS has "energygrps" option (or any other similar options)
>> for bonded interactions (E_bond, E_ang, E_dih) for different groups. Let's
>> say I have three different chains in a single box and I want to extract
>> the
>> bonded interactions for every chain separately. Would I be able to do that
>> on the fly during Gromacs run. I went through the webmanual and gmx_user
>> page but didn't find any solution for that. I would be very grateful if
>> someone could help me sharing how I could do this.
>>
>
> energygrps will do nothing for bonded terms.
>
> If you want bonded energies of individual components, you will have to
> strip out the coordinates you want from the trajectory (trjconv), make a
> corresponding .tpr file (convert-tpr) and use mdrun -rerun to compute the
> potential energy of that species. Note that these quantities are quite
> unlikely to have any physical meaning.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
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> http://www.thelemkullab.com
>
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-- 
Debdas Dhabal
Postdoctoral Researcher.
SEAS, Department of Chemical and Biomolecular Engineering,
The University of Pennsylvania, Philadelphia, PA 19104, USA.