[gmx-users] trjcat eneconv time continuation

[David Rodríguez]

2011/4/25 Tsjerk Wassenaar <tsjerkw at gmail.com>

> Hi David,
>
> You should have as many lines with a 'c' as you have trajectories.
>
> Cheers,
>
> Tsjerk
>
Sure Tsjerk!

Now options 2 and 3 (not 1) work, just that easy. Thank you so much.

Best,
David.

> On Apr 25, 2011 3:51 PM, "David Rodríguez" <david.rguez.diaz at gmail.com>
> wrote:
>
>
>
> 2011/4/25 Mark Abraham <Mark.Abraham at anu.edu.au> > > On 4/25/2011 8:42 PM,
> David Rodríguez wrote: >>...
>
> Sorry that my query wasn't detailed enough. Trjcat yields a Fatal error
> (Error reading user input). Here is what I tried, considering the first 2
> trajectories (the errors are the same if you consider more than that):
>
> Option 1:
> echo c | trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime
>
> Option 2:
> trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime << EOF
> c
> EOF
>
> Option 3:
> trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime < choice.txt
>
> Where 'choice.txt' contains the letter 'c' in one line.
> The log in any case is the following:
>
>
>
>                       :-)  /opt/gromacs405/bin/trjcat  (-:
>
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f      traj1.xtc  Input, Mult.
>           traj2.xtc               Trajectory: xtc trr trj gro g96 pdb cpt
>   -o   traj_1_2.xtc  Output, Mult. Trajectory: xtc trr trj gro g96 pdb
>   -n      index.ndx  Input, Opt.  Index file
> -demux     remd.xvg  Input, Opt.  xvgr/xmgr file
>
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    19      Set the nicelevel
> -tu          enum   ps      Time unit: ps, fs, ns, us, ms or s
> -[no]xvgr    bool   yes     Add specific codes (legends etc.) in the output
>                             xvg files for the xmgrace program
> -b           time   -1      First time to use (ps)
> -e           time   -1      Last time to use (ps)
> -dt          time   0       Only write frame when t MOD dt = first time
> (ps)
> -prec        int    3       Precision for .xtc and .gro writing in number
> of
>                             decimal places
> -[no]vel     bool   yes     Read and write velocities if possible
> -[no]settime bool   yes     Change starting time interactively
> -[no]sort    bool   yes     Sort trajectory files (not frames)
> -[no]keeplast  bool no      keep overlapping frames at end of trajectory
> -[no]cat     bool   no      do not discard double time frames
>
> Reading frame       1 time   50.000
>
>
> Enter the new start time (ps) for each file.
> There are two special options, both disable sorting:
>
> c (continue) - The start time is taken from the end
> of the previous file. Use it when your continuation run
> restarts with t=0.
>
> l (last) - The time in this file will be changed the
> same amount as in the previous. Use it when the time in the
> new run continues from the end of the previous one,
> since this takes possible overlap into account.
>
>           File             Current start (ps)  New start (ps)
> ---------------------------------------------------------
>                 traj1.xtc        0.000 ps
> traj2.xtc        0.000 ps
> -------------------------------------------------------
> Program trjcat, VERSION 4.0.5
> Source code file: gmx_trjcat.c, line: 178
>
> Fatal error:
> Error reading user input
> -------------------------------------------------------
>
> "Yeah, a Wuzz, Or a Jerk" (F. Black)
>
>
>
> This is with version 4.0.5, when using version 4.5 the log only differs in
> the line of the code where the error occurs (201 instead of 178).
>
> Best,
> David.
>
> > > Mark > > > > -- > gmx-users mailing list    gmx-users at gromacs.org >
> http://lists.gromacs.org/ma...
>
>
>
>
>
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