<br><div class="gmail_quote">2011/4/25 Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<p>Hi David,</p>
<p>You should have as many lines with a 'c' as you have trajectories.</p>
<p>Cheers,</p>
<p>Tsjerk</p></blockquote><div>Sure Tsjerk!<br>
<br>
Now options 2 and 3 (not 1) work, just that easy. Thank you so much.<br>
<br>
Best,<br>David.<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<p></p><blockquote type="cite">On Apr 25, 2011 3:51 PM, "David Rodríguez" <<a href="mailto:david.rguez.diaz@gmail.com" target="_blank">david.rguez.diaz@gmail.com</a>> wrote:<br><br><br><br><div class="gmail_quote">
<p><font color="#500050">2011/4/25 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>
>
> On 4/25/2011 8:42 PM, David Rodríguez wrote:
>>...</font></p><div><div></div><div class="h5"><div><br>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):<br><br>Option 1:<br><span style="font-family: courier new,monospace;">echo c | trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime</span><br clear="all">
<br>Option 2:<br><span style="font-family: courier new,monospace;">trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime << EOF</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">c</span><span style="font-family: courier new,monospace;"></span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">EOF</span><br><br>Option 3:<br><span style="font-family: courier new,monospace;">trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime < choice.txt<br><br><span style="font-family: arial,helvetica,sans-serif;">Where 'choice.txt' contains the letter 'c' in one line.<br>
The log in any case is the following:<br><br><br></span>
<br> :-) /opt/gromacs405/bin/trjcat (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f traj1.xtc Input, Mult.<br>
traj2.xtc Trajectory: xtc trr trj gro g96 pdb cpt<br> -o traj_1_2.xtc Output, Mult. Trajectory: xtc trr trj gro g96 pdb<br> -n index.ndx Input, Opt. Index file<br>-demux remd.xvg Input, Opt. xvgr/xmgr file<br>
<br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 19 Set the nicelevel<br>-tu enum ps Time unit: ps, fs, ns, us, ms or s<br>
-[no]xvgr bool yes Add specific codes (legends etc.) in the output<br> xvg files for the xmgrace program<br>-b time -1 First time to use (ps)<br>-e time -1 Last time to use (ps)<br>
-dt time 0 Only write frame when t MOD dt = first time (ps)<br>-prec int 3 Precision for .xtc and .gro writing in number of<br> decimal places<br>-[no]vel bool yes Read and write velocities if possible<br>
-[no]settime bool yes Change starting time interactively<br>-[no]sort bool yes Sort trajectory files (not frames)<br>-[no]keeplast bool no keep overlapping frames at end of trajectory<br>-[no]cat bool no do not discard double time frames<br>
<br>Reading frame 1 time 50.000<br><br><br>Enter the new start time (ps) for each file.<br>There are two special options, both disable sorting:<br><br>c (continue) - The start time is taken from the end<br>of the previous file. Use it when your continuation run<br>
restarts with t=0.<br><br>l (last) - The time in this file will be changed the<br>same amount as in the previous. Use it when the time in the<br>new run continues from the end of the previous one,<br>since this takes possible overlap into account.<br>
<br> File Current start (ps) New start (ps)<br>---------------------------------------------------------<br> traj1.xtc 0.000 ps traj2.xtc 0.000 ps<br>
-------------------------------------------------------<br>Program trjcat, VERSION 4.0.5<br>Source code file: gmx_trjcat.c, line: 178<br><br>Fatal error:<br>Error reading user input<br>-------------------------------------------------------<br>
<br>"Yeah, a Wuzz, Or a Jerk" (F. Black)<br><br><br><br><font face="arial,helvetica,sans-serif">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).<br><br>Best,<br>David.<br><br></font></span> </div></div></div><p><font color="#500050">>
> Mark
>
>
>
> --
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>
> <a href="http://lists.gromacs.org/ma." target="_blank">http://lists.gromacs.org/ma.</a>..</font></p></div><br><br clear="all"><br><br>
<br>--<div class="im"><br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></div></blockquote>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>