Re: [gmx-users] trjcat skipping frames
Jared James Thompson wrote: 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 This error is unrelated to what you're doing. The problem came with a combination of -b and -cat options to trjcat, neither of which you're using. The fix has been in place for some time, as noted in Berk's message (incorporated prior to the release of version 4.0). If you want help with your specific problem, please answer the questions I posed before. -Justin ~j Quoting "Justin A. Lemkul" : 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: FileStart time Time step - ftc_1.trr0.000 ps1.000 ps ftc_2.trr 20.000 ps0.000 ps ftc_3.trr 40.000 ps0.000 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 -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] trjcat skipping frames
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" : > > > 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: > > > > FileStart time Time step > > - > > ftc_1.trr0.000 ps1.000 ps > > ftc_2.trr 20.000 ps0.000 ps > > ftc_3.trr 40.000 ps0.000 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 listgmx-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
Re: [gmx-users] trjcat skipping frames
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: FileStart time Time step - ftc_1.trr0.000 ps1.000 ps ftc_2.trr 20.000 ps0.000 ps ftc_3.trr 40.000 ps0.000 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 -- gmx-users mailing listgmx-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
