[gmx-users] trjcat settime

Justin A. Lemkul jalemkul at vt.edu
Sat May 15 03:28:51 CEST 2010

nishap.patel at utoronto.ca wrote:
> Hello,
>    I have a concern regarding what -settime actually does. I ran 
> replicates of same simulation with different starting trajectories, 
> basically to get more sampling. Now I wish to combine all the .xtc files 
> from each replicates so I can analyze it as a whole. Now what's the 
> difference if I combine the .xtc files using just trjcat -f md.xtc 
> md1.xtc....mdN.xtc -o whole.xtc or if I use -settime option. Any 
> insights would be appreciated.

The -settime option lets you override whatever is written in the trajectory as 
far as the starting time is concerned.  So if you have several trajectories that 
all start at zero, if you try to concatenate them, trjcat will simply over-write 
frames that have duplicate times instead of actually concatenating them.

Beware that if you're trying to concatenate different trajectories end-to-end, 
if you have, for 10-ns trajectories, and you use -settime to keep md1.xtc at 0, 
then md2.xtc at 10000 (ps), the frame from md2.xtc will be retained for the 
frame at 10000 ps, over-writing the frame at 10000 ps in md1.xtc.  Beware.


> Thanks
> Nisha P


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list