On 7/18/12 9:34 AM, James Starlight wrote:
Justin
thanks for advise
I've used the bellow command for both trajectory
trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc
but resulted merged_noPBC.xtc consist of data from only second
trajectory although in the log file both trajectories have been
processed
File Current start (ps) New start (ps)
---------------------------------------------------------
md_noPBC.xtc 0.000 ps 0
md_noPBC_GO.xtc 0.000 ps 0
Summary of files and start times used:
File Start time Time step
---------------------------------------------------------
md_noPBC.xtc 0.000 ps 7.000 ps
md_noPBC_GO.xtc 0.000 ps 7.000 ps WARNING:
same Start time as previous
Back Off! I just backed up merged_noPBC.xtc to ./#merged_noPBC.xtc.5#
Reading frame 0 time 0.000
Reading frame 3000 time 21000.000
Reading frame 0 time 0.000
Continue writing frames from md_noPBC_GO.xtc t=0 ps, frame=0
Reading frame 10000 time 70000.000 -> frame 10000 time 70000.000 ps
Last frame written was 10008, time 70056.000000 ps
Why this occurs ?
Because you're telling trjcat that both trajectories start at the same time, so
they're going to overwrite one another. If they are indeed two separate
segments of a continuous trajectory, they need different start times, one zero
and one non-zero.
By the way if I'm using -cat option resulted file consist of both
trajectories ( in the separate enties).
That's what -cat is designed to do. I doubt you want that in this case. The
times will still be wrong.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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