[gmx-users] trjcat: joining randomized PDB files

Anirban reach.anirban.ghosh at gmail.com
Thu May 9 15:49:19 CEST 2013

Thanks a lot Justin, for the reply.
But with -settime for every file I have to interactively give arbitrary
values. I have around 500 PDB files for one part of the trajectory and
there are total 10 parts. So its very difficult to repeat this for around
5000 times. Is there any other option. trjcat reads the randomized PDB
files serially, so can't it just concatenate the files in that order? Or am
I missing something?

Thanks again.



On Thu, May 9, 2013 at 7:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 5/9/13 9:35 AM, Anirban wrote:
>> Dear ALL,
>> I want to randomize the frames of my trajectory for calculating
>> convergence. For this, I have dropped the frames as PDB files using
>> trjconv
>> and then renamed them randomly. Now I want to join these randomized PDB
>> frames to get a randomized trajectory using trajcat. But somehow trjcat
>> always joins them in proper frame order (inspite of completely random PDB
>> file names). How can I join the randomly to get a randomized trajectory?
>> Any suggestion is welcome.
> Use -settime and give them arbitrary time values.
> -Justin
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