[gmx-developers] rebuild the .traj file from .gro files

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 20 00:48:40 CET 2009

Ana West wrote:
> Hello,
> I ran a series of important simulations and I do not have my topol.tpr 
> or traj.trr files anymore. I do however still have the confout.gro files 
> for all the frames composing my trajectories. Is there a way for me to 
> reconstruct my traj.trr files and the topol.tpr files from the  
> confout.gro files and topol.top files?

You have already lost precision in the conversion to the 
limited-precision ASCII format, and probably you also have not kept any 
velocities, etc. This will mean you cannot restart the simulation. 
There's probably no purpose served by merely converting the information 
in the .gro format to .trr format, but you can do that with trjconv. You 
can also generate a .tpr file from your .top file, .mdp file and a .gro 
file, but you will need a source of velocities, and it would not be an 
exact match of the original .tpr file made at that point even if you had 
the right velocities. See http://wiki.gromacs.org/index.php/Doing_Restarts

> Using gmxdump I learned of the type of information contained in a binary 
> .tpr and .trr file. However, I do not seem to figure out how to convert 
> the ASCII files to their corresponding binary files. Do you guys have 
> any suggestions for me?

Not ones that will help with your immediate problem. Careful planning, 
execution and backups are important.


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