>Send gmx-users mailing list submissions to > gmx-users@gromacs.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users >or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > >You can reach the person managing the list at > [EMAIL PROTECTED] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gmx-users digest..." > > >Today's Topics: > > 1. Re: Incomplete header: nr 3078 time 9408 (David van der Spoel) > 2. Re: trjorder does not write trajectory file (Dmytro Kovalskyy) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sun, 11 Nov 2007 09:41:35 +0100 >From: David van der Spoel <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Incomplete header: nr 3078 time 9408 >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=UTF-8; format=flowed > >Dechang Li wrote: >> Dear all, >> >> I used Gromacs-3.3.1 to do a simulation. When it finished, I used >> command "g_dist" to calculate two groups distance VS time. But at time >> 9408ps, it stopped and showed " Incomplete header: nr 3078 time 9408". >> My simulation is 12ns longer. What is the problem? How can I resolve it? >> >> >start by testing the trajectory with gmxcheck I did what you said. Following is the message:
Reading frame 3000 time 9254.000 Warning at frame 3077. Velocities for atom 11896 are large (52568.4) Warning at frame 3077. Velocities for atom 11896 are large (7.68295e+31) Warning at frame 3077. Velocities for atom 11896 are large (2.75578e+23) Warning at frame 3077. Velocities for atom 11901 are large (9410) WARNING: Incomplete header: nr 3078 time 9408 Item #frames Timestep (ps) Step 3078 2 Time 3078 2 Lambda 3078 2 Coords 3078 2 Velocities 3078 2 Forces 0 Box 3078 2 Did it mean my simulation was failed? But I have checked the energy file "ener.edr", too. The energy file seems fine. How did it happen? Can I use the date after time 9254ps? >> Best regards, >> >> 2007-11-11 >> ������������������������ >> >> ========================================= >> Dechang Li, PhD Candidate >> Department of Engineering Mechanics >> Tsinghua University >> Beijing 100084 >> PR China >> >> Tel: +86-10-62773779(O) >> Email: [EMAIL PROTECTED] >> =========================================��������������� >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 > > >-- >David. >________________________________________________________________________ >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, >Dept. of Cell and Molecular Biology, Uppsala University. >Husargatan 3, Box 596, 75124 Uppsala, Sweden >phone: 46 18 471 4205 fax: 46 18 511 755 >[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > >------------------------------ > >Message: 2 >Date: Sun, 11 Nov 2007 13:01:19 +0200 (EET) >From: "Dmytro Kovalskyy" <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] trjorder does not write trajectory file >To: "Justin A. Lemkul" <[EMAIL PROTECTED]> >Cc: gmx-users@gromacs.org >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain;charset=utf-8 > >> It works fine for me under 3.3.1 - what command line are you issuing? >trjorder -f traj.xtc -s topol.tpr -o 5A -nshell 5A -r 0.5 >> >> -Justin >> >> Quoting Dmytro Kovalskyy <[EMAIL PROTECTED]>: >> >>> >>> Trjorder does not write trajectory file, only nshell.xvg >>> >>> This is true for 3.3.2 and 3.3.1 versions. >>> >>> Dima >>> >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 >>> >> >> >> >> ========================================================= >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> [EMAIL PROTECTED] | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> >> ========================================================= >> >> >> !DSPAM:47367e03304461801161890! >> >> > > > > >------------------------------ > >_______________________________________________ >gmx-users mailing list >gmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! > >End of gmx-users Digest, Vol 43, Issue 42 >*****************************************
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