Re: [gmx-users] Concatenating trajectories
... and next time you might be better served by using gmx mdrun -cpi and gmx trjconv -extend so that you have your contiguous trajectory by construction! Mark On Thu., 9 Apr. 2020, 14:17 Qinghua Liao, wrote: > Hello, > > There is an option of -settime for gmx trjcat, with which you can set > different starting simulation time > for each trajectory. > > > All the best, > Qinghua > > On 4/9/20 1:26 PM, Pandya, Akash wrote: > > Hi, > > > > I have four trajectories of the same condition (protein only) that I > want to concatenate. I used the command below to do this: > > > > gmx trjcat -f Traj1.xtc Traj2.xtc Traj3.xtc Traj4xtc -o TrajFINAL.xtc > -cat > > > > So this command gives me a file with all four trajectories, pasted > together. The combined trajectory has now got four sets of the same time > stamps. My question is how can I change the time stamps so that they appear > in chronological order, instead of repeated time stamps?. So I would have a > combined trajectory e.g. 20 to 200 ns. > > > > I hope I'm being clear about what I want to do and someone can guide me > on achieving this. > > > > Best wishes, > > > > Akash > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Concatenating trajectories
Hello, There is an option of -settime for gmx trjcat, with which you can set different starting simulation time for each trajectory. All the best, Qinghua On 4/9/20 1:26 PM, Pandya, Akash wrote: Hi, I have four trajectories of the same condition (protein only) that I want to concatenate. I used the command below to do this: gmx trjcat -f Traj1.xtc Traj2.xtc Traj3.xtc Traj4xtc -o TrajFINAL.xtc -cat So this command gives me a file with all four trajectories, pasted together. The combined trajectory has now got four sets of the same time stamps. My question is how can I change the time stamps so that they appear in chronological order, instead of repeated time stamps?. So I would have a combined trajectory e.g. 20 to 200 ns. I hope I'm being clear about what I want to do and someone can guide me on achieving this. Best wishes, Akash -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Concatenating trajectories
Hi, I have four trajectories of the same condition (protein only) that I want to concatenate. I used the command below to do this: gmx trjcat -f Traj1.xtc Traj2.xtc Traj3.xtc Traj4xtc -o TrajFINAL.xtc -cat So this command gives me a file with all four trajectories, pasted together. The combined trajectory has now got four sets of the same time stamps. My question is how can I change the time stamps so that they appear in chronological order, instead of repeated time stamps?. So I would have a combined trajectory e.g. 20 to 200 ns. I hope I'm being clear about what I want to do and someone can guide me on achieving this. Best wishes, Akash -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
