[email protected] 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.
-Justin
Thanks
Nisha P
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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