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

Justin Lemkul jalemkul at vt.edu
Sat May 19 01:55:25 CEST 2018

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 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


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