[gmx-users] trjcat

[Justin A. Lemkul]

rams rams wrote:
> Dear Users,
> 
> I tried to create a trajectory file from a set of pdb files (infact 
> several of them) starting from time frame 0 to lets say 100 with an 
> interval of 1ps each. If I use the following command,
> 
> trjconv -f  0.xtc 1.xtc ......100.xtc -o .xtc
> 
> its resuling only one frame (I think its not stiching them).
> 
> If I use "-settime" along with the above command, it is stiching all the 
> frames, but its asking for the start time for each frame. Its really 
> difficult to mention the start times for several hundred frames. Is 
> there any way we can handle this.
> 

The best way to do this would be to develop a script to do it for you.  Assuming 
you have files named like frame_0.pdb, frame_1.pdb, etc:

#!/bin/bash

for file in `ls | grep frame`; do

         temp=${file#frame_}
         num=${temp%.pdb}

	trjconv -f $file -s $file -o traj_$file -t0 $num

done

(Haven't tested that, so it might not be perfect)

Then they frames (now called, for example, traj_frame_0.pdb) can be assembled 
with trjcat, without having to specify -settime, since trjconv will have 
assigned them a time value.

-Justin

> Thanks.
> Ram.
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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