What I meant is: do you save the trajectory every 0.1ps? The problem seem to be that trjconv isn't able to find any frame between t=0.1ps and t=0.2ps. So, if you save you data every 1ps, there's no data in your .xtc file. This is why Xavier suggested to use gmxcheck, that will tell you both how many steps you have in the xtc and what's the timestep.
I agree that trjconv is more convenient than VMD for this. Ran. OZGE ENGIN wrote: > Of course, I am performing a 40 ns simulation, and 14 ns of it has been > finished. > > What may be the problem? I know, I can extract specific frames via VMD, but > it changes atom types after saving in pdb format. > > -----Original Message----- > From: Ran Friedman <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <[email protected]> > Date: Mon, 19 Nov 2007 17:53:16 +0100 > Subject: Re: [gmx-users] trjconv does not work > > I see. Do you have any structure between t=0.1ps and t=0.2ps? > > Ran. > > OZGE ENGIN wrote: > >> The command line ws the following: >> >> trjconv -s peptide_b4md.gro -f traj.xtc -b 0.1 -e 0.2 -o file_1.pdb >> >> >> > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >
_______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
