Thanks Justin,
On Wed, Feb 10, 2010 at 8:49 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Segun Jung wrote: > >> Dear gromacs users, >> >> I am trying to collect trajectories corresponding to each temperature by >> using trjcat with demux. >> >> There were similar issues posted earlier, but I do not see the solution on >> the problem I am facing following: >> >> > Like what? It will save time if you can post links to these "similar > issues" to avoid posting non-solutions that have already been ruled out. > > > I have 64 replicas simulated using namd in dcd trajectory format and >> saved them in gromacs format (.trr) using vmd. >> >> I inspected the gromacs format trajectories by eyes in vmd and looked >> fine. However, when I tried trjcat -f g*.trr -demux replica_index.xvg, >> >> the output looked weird. So I tested a small set of the trajectories >> (using only replicas 0 to 8 and first two frames) and >> >> noticed that the output does not match to the replica_index.xvg file. >> >> > If you ran your simulations with NAMD, how did you generate this file? In > Gromacs, one would run demux.pl on the md.log file. I presume NAMD prints > different output. > > I wrote a perl script which does the same job as demux.pl generating the replica_index.xvg. > > >> trjcat -f *g*.trr -demux replica_index.xvg >> >> replica_index.xvg >> >> 0 0 1 2 3 4 5 7 6 >> >> 2 1 0 2 3 5 4 6 7 >> >> > If you analyzed replicas 0 to 8 (inclusive) then you should have an 8 > somewhere, right? And I was testing 8 replicas (from 0 to 7). Sorry about the confusion. > > > >> I am using Ubuntu (32bit) and the gromas version is 4.0.5. >> >> 0_trajout.xtc should have the 1st frame from replica 0 and 2nd frame from >> replica 1, but both frames for 0_trajout.xtc are from the replica 0. >> >> > This might go along with my comment above. If there are nine replicas (0 > to 8), then there may be some mis-translation of the .xvg file. > > > It seems the index file does not cooperate properly with the trjcat and >> -demux. Does anyone have clue about this? >> >> > I know I can attest to demultiplexing working as advertised, so I assume > intact trajectories with a correct index file should work properly. You > have a few variables to deal with: .dcd->.trr translation, however you > generated the .xvg file, and if you've even told us the right number of > replicas, among perhaps others. > I fixed a minor mistake in my perl script which generates replica_index.xvg and it works fine except the time step 0 of input file (*.trr) is saved two times in the output file (*.xtc) although rest of the trajectories are okay. -Segun > > Also, what does gmxcheck tell you about each of the .trr files? Do they > contain what you would expect them to? > > -Justin > > >> Many thanks, >> >> Segun >> >> > -- > ======================================== > > 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 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 > -- --------------------------------------- Segun Jung, Ph.D. Candidate Computational Biology Schlick Lab, Department of Chemistry New York University http://homepages.nyu.edu/~sj801 ----------------------------------------
-- 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
