The old information is given below. I haven't chopped into the code yet to see if Berk's fix is there.
http://www.mail-archive.com/gmx-users@gromacs.org/msg14689.html ~j Quoting "Justin A. Lemkul" <jalem...@vt.edu>: > > > Jared James Thompson wrote: > > Hi All, > > > > I'm having a problem with trjcat skipping frames. I saw a similar > complaint > > seemingly handled by Berk Hess in 2008. I wanted to know if his bug fix has > been > > incorporated into the current gromacs version. > > > > Can you provide a link to this information? What version of Gromacs are you > > using? Presumably, if you're using the latest version, bugs from 2 years ago > > should be fixed. > > > I have a number of short .trj files of equal length and time spacing that I > want > > to cat together to form a single .trj file. I have a method for doing this > using > > trjcat and trjconv. It has worked normally in the past. > > > > The method is as follows. Set the start time of each trajectory to be the > next > > putative frame immediately following the previous trajectory, and also set > the > > timestep for each frame correctly, so for .trj of 10 frames long: > > > > trjconv -f frame_traj_2.trr -o ftc_2.trr -t0 20 -timestep 1.0 > > > > trjconv -f frame_traj_3.trr -o ftc_3.trr -t0 30 -timestep 1.0 > > > > etc. > > > > Once all the frame_traj_x files are together, then use trjcat to cat them. > > > > trjcat -f ftc* -o CombinedTraj.trj > > > > > > However, this time that I am using it, trjcat is producing the following > > response, note the timestep shown in the File Roster and that ftc_5 is > treated > > normally for some reason: > > > > File Start time Time step > > --------------------------------------------------------- > > ftc_1.trr 0.000 ps 1.000 ps > > ftc_2.trr 20.000 ps 0.000 ps > > ftc_3.trr 40.000 ps 0.000 ps > > Clearly something has broken down on a very fundamental level. You set > ftc_3.trr to have a start time of 30 ps above, but it has not worked. > > Some questions that may help diagnose your issue: > > 1. What is the spacing of frames in your original .trr files? > 2. What does gmxcheck tell you about each of your ftc_*.trr files? > 3. Does passing -t0 and -timestep to trjconv in separate steps make any > difference? > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
