[CP2K-user] How to remove repeated entries in -pos-1.xyz file from MetaD simulation?

Travis polla... at gmail.com
Wed Apr 17 21:37:10 UTC 2019


CP2K adds the simulation time and timestep to the header. Use that info to 
make a script that identifies and deletes repeats in increments of (#atoms 
+ 2). You can identify repeats with grep easily enough, grep " i = .* 
$frm\," where $frm is an increment over frames in a loop, i.e., for 
((frm=0; frm<=$frames; frm+=$increment)). You can either delete repeated 
entries or rewrite your trajectory to skip repeated frames. Just be sure to 
keep a backup of your original trajectory just in case something goes wrong.


On Wednesday, April 17, 2019 at 2:20:28 PM UTC-4, Raghav wrote:

> Dear all,
> I'm running a *Metadynamics* simulation and I *restarted* my calculations 
> many times, as a result I have a lot of *repeated* entries in my -
> pos-1.xyz file.  For e.g steps 21 to 29 are repeated in the attached file 
> as a result of restarting.
> I have to perform analysis on the trajectory but for that I need to remove 
> the *repeated *entries. Does anyone know how to do this? 
> My system is very large and the trajectory as well, hence doing this 
> manually is a daunting task.
> Thanks and Regards,
> Raghav
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