[gmx-users] trjcat eneconv time continuation

David Rodríguez david.rguez.diaz at gmail.com
Mon Apr 25 15:50:33 CEST 2011

2011/4/25 Mark Abraham <Mark.Abraham at anu.edu.au>

> On 4/25/2011 8:42 PM, David Rodríguez wrote:
>> Hi,
>> I am dealing with a special case of trajectory concatenation: I have
>> several equilibration trajectories that their times are always restarted to
>> 0, due employing different force constants for positional restraints, but
>> using the output structure of the previous step as input anyway. Using
>> trjcat, it obviously works when you do:
>> trjcat -f traj1.xtc traj2.xtc traj3.xtc traj4.xtc traj5.xtc traj6.xtc -o
>> traj_all.xtc -settime
>> and you interactively introduce 'c' (continue) for each case (there are no
>> overlapping frames). I haven't found a way to continue the trajectory times
>> without using -settime (neither -cat nor -keeplast), with both versions
>> 4.0.7 or 4.5. At the same time, I've tried to introduce the 'c' value in a
>> non-interactive way (as indicated in
>> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive)
>> when using -settime, but it doesn't recognize it.
>> I was wondering if there is a way to make the above mentioned command-line
>> to work non-interactively. The same applies for the eneconv tool when
>> concatenating .edr files.
> Unfortunately, the advice you'd get from people here on the topic of how to
> make such commands work non-interactively is already on the link you
> provided. You're more likely to get effective help if you say exactly what
> you did and how you observed "it doesn't recognize it".

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

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).


> Mark
> --
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