Hi Justin, In many of the frames, if I use -b and -e to be same , it works For example, I found if I use -b 16 -e 16, it gives me the the snapshot at 16ps. But, in many cases like 14ps, it is not working. Also, I tried -b 13 -e 14 -dump 14 . It does not work saying 'WARNING no output, trajectory ended at 14' Any help will be appreciated. Sanku
________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Thu, May 5, 2011 10:22:38 AM Subject: Re: [gmx-users] trjconv problem Sanku M wrote: > Hi, > I am having a problem with trjconv to get a single snap-shot from a >trajectory file. I am using gromacs 4.0.7 . > If I try to get a snapshot corresponding to 14 ps, I was trying to use "-b > 14 >-e 14 " command as follows. But, > If I issue this command as shown below > trjconv --f traj.xtc -o conf_pep.gro -s topol.tpr -b 14.0 -e 14.0 it >crashes with following error: > Precision of traj.xtc is 0.001 (nm) > Using output precision of 0.001 (nm) > > WARNING no output, trajectory ended at 14 > > However, if I issue the same trjconv command using "-dump 14" as shown below, >trjconv provides the correct snapshot at 14 ps: > trjconv --f traj.xtc -o conf_pep.gro -s topol.tpr -dump 14.0 But, this >"-dump 14" command becomes extremely time consuming as I was trying to get the >snap-shot for a long time i.e around 30000ps . So, I am trying to get "-b 14 >-e >14" command work . So, I was wondering whether you have any clue how to get >around with this. If I recall, -b and -e cannot be the same. This is the reason for -dump. It might be worth a try to see if trjconv -b 13 -e 14 -dump 14 speeds things up any. -Justin > Sanku > > -- ======================================== 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/Support/Mailing_Lists/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/Support/Mailing_Lists
-- 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/Support/Mailing_Lists/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/Support/Mailing_Lists