[gmx-users] convert .tpr to include energy groups

Justin Lemkul jalemkul at vt.edu
Wed Aug 9 03:03:03 CEST 2017

On 8/8/17 4:03 PM, Tushar Ranjan Moharana wrote:
> Hi All,
> I want to calculate interaction between 2 energy groups, which were not
> defined during the run. So I want to rerun and include both the energy
> groups while rerunning. This can be easily done by again assembling .tpr
> file from .gro, .top and .cpt file by grompp, but I donot have the .gro and
> .cpt file, which I used to compile the original .tpr file. I have topology
> file and run input (.tpr) file and the new trajectory obtained after
> running .tpr file.
> Can I convert old .tpr to include energy groups or can I get .cpt and .gro
> used to compile the .tpr file?

You don't need a checkpoint file to regenerate a .tpr to recalculate energies. 
You can extract the original coordinates from the .tpr using editconf.  Then 
process an .mdp with appropriate energygrps to generate a .tpr for the purpose 
of running mdrun -rerun.



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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