[gmx-users] reg:merging of files

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 1 23:51:57 CEST 2008

rams rams wrote:
> Dear users,
> I have a general question regarding the merging of files:
> 1. If suppose I am rerunning a job, the new tpr file is created in the 
> following way:
> tpbconv -s .tpr1 -f .trr1 -o .tpr2
> Here, no confusion. The run with new tpr2 would give me .trr2 file.
> Now if I want to rerun again,
> tpbconv -s tpr2 -f trr2 -o tpr3.
> In case, if I merge trr1 and trr2 to trr_total, and want to use the 
> merged file to rerun, which tpr I shoud use for creating a new tpr file 
> ? Precisely,
> tpbconv -s ???? -f trr_total  -o tpr3

Either one really.  The important bits of information from the .tpr file are the 
parameters from the topology (bonded and nonbonded), all the different molecule 
definitions, and the .mdp parameters, which are generally constant during 
production runs.  Coordinates and velocities are read from the .trr file.

Don't forget to include the .edr file to get an exact continuation if you are 
applying temperature and/or pressure coupling!

> Also, for analysis, do we need to merge all the tpr files or only the 
> starting tpr file is enough ? What information exactly the tpr file holds ?

You cannot merge .tpr files.  Do a gmxdump on your .tpr and you will see that 
there are no time-dependent quantities to stitch together.


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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