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

[Justin Lemkul]

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

-- 
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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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