[gmx-users] trjconv t0/timestep parameter confusion
mark.abraham at anu.edu.au
Mon Oct 25 15:36:44 CEST 2010
Maybe these parameters do not work in concert. Try a two-pass version - first discard the first 10000, then later relabel the times.
----- Original Message -----
From: Martin Hoefling <mhoefli at gwdg.de>
Date: Tuesday, October 26, 2010 0:29
Subject: [gmx-users] trjconv t0/timestep parameter confusion
To: gmx-users at gromacs.org
> Hey Folks,
> I am having trouble with the t0 parameter in conjunction with -
> b. What I am trying to obtain is the following: Trajectory
> starts at 0 ends at 110000. From this trajectory, I wanna write
> out frames from 10000 to 110000 (so discard the first 10000) and
> set starting time to 0 so that I get a trajectory from 0 to 100000.
> What I tried is the following: trjconv -f in.xtc -b 10000 -t0 0 -
> o out.xtc
> This leads to a never ending trjconv process writing out a
> trajectory with frames and a deltat of 0.
> Did I misunderstood the parameters somehow? Tested with 4.0.7
> and 4.5, time units are ps and trajectories have 1ps sampling.
> Best wishes
> The workaround for this problem:
> First writing -b into a temp trajectory and then treating the
> tmp trajectory with -t0 0
> Martin Hoefling
> Max Planck Institute for Biophysical Chemistry
> Theoretical & Computational Biophysics
> Am Fassberg 11
> 37077 Goettingen
> Phone: +49 551 201 2314
> Fax: +49 551 201 2302
> Mail: mhoefli at gwdg.de
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