[gmx-users] trjconv -dt issue

Matthias Ernst matthias.ernst at physik.uni-freiburg.de
Wed Aug 19 23:50:21 CEST 2015


I have a quite long continuous trajectory coming from several initial
input pieces (cluster crashed...) that I want to downsample, as a start
from 0.5ps timestep in the source files to just 1ps and later bigger

Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be
rounding issues which leads to times at .5ps being written from some
timestamp on (4.1943e+06). Is this a known behaviour?

Related to this, what does the following sentence in the help for
trjconv -dt mean:
"This option relies on the accuracy of the times in your input
trajectory, so if these are inaccurate use the -timestep option to
modify the time (this can be done simultaneously)."
How can I change the input timestep to get a "proper" output of output
frames? I tried to use -timestep 1 it to my trajectory with 0.5ps
timestep and it seems to produce "correct" timestamps in 1ps steps in
the output file but the coordinates still are those of the initial
frames with the 0.5ps timestamps, meaning it just relabels the
timestamps of the frames. Using "-timestep 0.5 -dt 1" together does not
change the result compared to "-dt 1" only.

If I rather use the "-t0 0" option, I can "reset" the time of the first
frame and then, it looks like it writes the "correct" 1ps stepped frames
with 1ps timestamps, but starting at time 0. As I have several
trajectory pieces from a continuous timeseries to concatenate, I would
have to run trjconv once more just to correct and "reset" the time to
its initial value, which means a lot of unnecessary data transfer,
especially in the case of long trajectories.
Is this really necessary or is there another way to get a "proper"
I know I can use  the -skip 2 option but e.g. not for eneconv which only
supports -dt and has the same issues. Further, just using -skip 2 is not
possible if some input files are at 0.5ps, but some other already at 1ps
time steps.

Thank you for your help,

Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611

More information about the gromacs.org_gmx-users mailing list