Re: Combining trajectories

From: David Konerding <>
Date: Wed 28 Mar 2001 08:10:30 -0800

Peter Varnai writes:
>Ptraj can combine trajectories with the following commands:
>trajin one.trj
>trajin two.trj
>[some operations like strip etc]
>trajout three.trj
>But this file will include the box size after each coord sets,
>which carnal and visualization programs don't like, so you should
>remove them with something like awk:
>(((NR-1)%236!=0) {print($0)}' three.trj > three_nobox.trj

No, for this, you could just use the ptraj "nobox" option:

trajin one.trj
trajin two.trj
trajout three.trj nobox

>I must admit, I could not get carnal combine trajectories as it was
>suggested in the examples:
>STREAM s1 a1.trj a2.trj a3.trj;
>due to segmentation fault...
>I hope this helps!
>Peter Varnai
>PS: have you tried the unix merge command to combine big files or
> cat file1 file2 > file3

That won't work, the file2 starts with a title, and you end up with a title embedded within your
trajectory. Perhaps judicious use of the head or tail command would let you do this.
Received on Wed Mar 28 2001 - 08:10:30 PST
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