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

[Debdas Dhabal]

Hi Justin,

When I follow the method you suggested I am getting an error.
(1) Using trjconv I have created a .trr file containing the coordinates of
the component for which I want to calculate the bonded energy.
(2) Now when I do *tpbconv_mpi -s topol.tpr (old tpr file) -f traj.trr
(containing component of my interest) -o tpxout.tpr *,  it is showing an
error message -> "Number of atoms in Topology is not same as in
Trajectory".

This means the trr file I am supplying should contain the trajectory of
whole system. If I do that then during *mdrun -s tpsout.tpr -rerun traj.trr*,
it is giving energy for whole system not for that single component. It
would be very nice if you could kindly help me resolving this error.

Thank you very much

With regards

On Fri, May 18, 2018 at 4:23 PM, Debdas Dhabal <ddhabal at seas.upenn.edu>
wrote:

> 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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> 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.
>



-- 
Debdas Dhabal
Postdoctoral Researcher.
SEAS, Department of Chemical and Biomolecular Engineering,
The University of Pennsylvania, Philadelphia, PA 19104, USA.