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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Do you really want to plainly cat the trajectories?<br>In that case the unix cat command would also do the trick.<br><br>trjcat -cat does not remove double frames, but does seem to remove<br>frames with time before the last written frame.<br><br>I found and fixed a bug in trjcat (fix is only in the CVS head tree)<br>where trjcat would skip frames with -b when some files were not used.<br></div>I pasted the fix below.<br>You can try to see if it also solves your problem.<br><br>Berk.<br><br>In gmx_trjcat.c replace the if (i >0) { ... } with the code below.<br><br> /* set the next time from the last frame in previous file */<br> if (i > 0) {<br> if (frame_out >= 0) {<br> if(cont_type[i]==TIME_CONTINUE) {<br> begin =frout.time;<br> begin += 0.5*timestep;<br> settime[i]=frout.time;<br> cont_type[i]=TIME_EXPLICIT; <br> }<br> else if(cont_type[i]==TIME_LAST) {<br> begin=frout.time;<br> begin += 0.5*timestep;<br> }<br> /* Or, if the time in the next part should be changed by the<br> * same amount, start at half a timestep from the last time<br> * so we dont repeat frames.<br> */<br> /* I don't understand the comment above, but for all the cases<br> * I tried the code seems to work properly. B. Hess 2008-4-2.<br> */<br> }<br> /* Or, if time is set explicitly, we check for overlap/gap */<br> if(cont_type[i]==TIME_EXPLICIT) <br> if( ( i < nfile_in ) &&<br> ( frout.time < settime[i]-1.5*timestep ) ) <br> fprintf(stderr, "WARNING: Frames around t=%f %s have a different "<br> "spacing than the rest,\n"<br> "might be a gap or overlap that couldn't be corrected "<br> "automatically.\n",convert_time(frout.time),time_unit());<br> }<br><br><br><hr id="stopSpelling">> Date: Fri, 11 Jul 2008 15:57:54 +0200<br>> From: michel.cuendet@isb-sib.ch<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] trjcat -cat skips frames<br>> <br>> <br>> Hi all,<br>> <br>> I have 162 small independent trajectories (from time 100 to time 300ps, <br>> 2ps interval) in directories named 1/ ... 162/. I want to merge them <br>> into one big trajectory for analysis purposes:<br>> <br>> trjcat -cat -o traj_tot.xtc -f */traj.xtc<br>> <br>> trjcat seems to start skipping some frames after about the 100th <br>> trajectory. It does not start reading at time 100 anymore. Total number <br>> of frames is 15432 instead of the 162*101 = 16632 that it should be. <br>> Output looks like below.<br>> <br>> Concatenating the trajectories in two batches of about 80 trajectories <br>> each and then combining the two resulting files together works.<br>> <br>> Cheers,<br>> Michel<br>> <br>> ===================================================================<br>> <br>> Reading frame 0 time 100.000 <br>> <br>> Continue writing frames from 100/traj.xtc t=100 ps, frame=0 <br>> Last frame 100 time 300.000 -> frame 100 time 300.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> <br>> Continue writing frames from 101/traj.xtc t=100 ps, frame=101 <br>> Last frame 100 time 300.000 -> frame 200 time 298.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> <br>> <br>> [ ... normal output until... ]<br>> <br>> <br>> Continue writing frames from 44/traj.xtc t=100 ps, frame=10100 <br>> Last frame 100 time 300.000 -> frame 10200 time 300.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> <br>> Continue writing frames from 45/traj.xtc t=100 ps, frame=10201 <br>> Last frame 100 time 300.000 -> frame 10300 time 298.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> Reading frame 1 time 102.000 <br>> Continue writing frames from 46/traj.xtc t=102 ps, frame=10302 <br>> Last frame 100 time 300.000 -> frame 10400 time 298.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> Reading frame 1 time 102.000 <br>> Continue writing frames from 47/traj.xtc t=102 ps, frame=10402 <br>> Last frame 100 time 300.000 -> frame 10500 time 298.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> Reading frame 2 time 104.000 <br>> Continue writing frames from 48/traj.xtc t=104 ps, frame=10502 <br>> Last frame 100 time 300.000 -> frame 10600 time 300.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> Reading frame 2 time 104.000 <br>> Continue writing frames from 49/traj.xtc t=104 ps, frame=10601 <br>> Last frame 100 time 300.000 -> frame 10690 time 282.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> Reading frame 3 time 106.000 <br>> Continue writing frames from 4/traj.xtc t=106 ps, frame=10700 <br>> Last frame 100 time 300.000 -> frame 10790 time 286.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> Reading frame 3 time 106.000 <br>> Continue writing frames from 50/traj.xtc t=106 ps, frame=10798 <br>> Last frame 100 time 300.000 -> frame 10890 time 290.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> <br>> [ ... more drifting the first frame read until ... ]<br>> <br>> Reading frame 30 time 160.000 <br>> Continue writing frames from 99/traj.xtc t=160 ps, frame=15290 <br>> Last frame 100 time 300.000 -> frame 15360 time 300.000 ps <br>> Reading frame 0 time 100.000 <br>> lasttime 300<br>> Reading frame 30 time 160.000 <br>> Continue writing frames from 9/traj.xtc t=160 ps, frame=15361 <br>> Last frame 100 time 300.000 -> frame 15430 time 298.000 ps <br>> <br>> Last frame written was 15431, time 300.000000 ps<br>> <br>> ===================================================================<br>> <br>> <br>> ==========================================================<br>> Michel Cuendet, Ph.D<br>> Molecular Modeling Group<br>> Swiss Institute of Bioinformatics<br>> CH-1015 Lausanne, Switzerland<br>> http://ludwig-sun1.unil.ch/~mcuendet<br>> ==========================================================<br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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