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

[Debdas Dhabal]

Thanks so much Justin.

With regards
Debdas

On Fri, May 18, 2018 at 7:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/18/18 6:08 PM, Debdas Dhabal wrote:
>
>> 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.
>>
>
> There is no need for a trajectory when creating a new .tpr file - that's
> an antiquated method for extending simulations.
>
> All you need is:
>
> tpbconv -s old.tpr -o new.tpr (with a suitable selection that may or may
> not require an index file)
>
>
> -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.