Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, please do so. In any case, try to feel more confident about yourself. You made it to academia already, didn't you?
Cheers, Tsjerk On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal < sonali11dhind...@yahoo.co.in> wrote: > Hello Sir, > Thanks for the reply, > I tried to run this commad on a simuation which I started to ran for 10 > ns,and has already completed around 3 ns > I gave > trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep > > after this it asked for selecting which one I want among, System, > protein,bacakbone,c-alpha etc, I selected system, and the output is three > files, namely > 1ns0.pdb > 1ns1.pdb > 1ns2.pdb > 1ns3.pdb > > Am I doing it correct ? > > Thanks > -- > Sonali Dhindwal > > > --- On *Fri, 16/7/10, David van der Spoel <sp...@xray.bmc.uu.se>* wrote: > > > From: David van der Spoel <sp...@xray.bmc.uu.se> > Subject: Re: [gmx-users] to visualise protein conformation after every 1ns > > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Friday, 16 July, 2010, 12:34 PM > > > On 7/16/10 9:02 AM, sonali dhindwal wrote: > > Hello All, > > Sorry for a dumb question,,but I have a query that I want to run a 5 ns > > simulation on one of the protein and I want to see protein's > > conformation after every 1 ns,i.e to have a pdb file, so how should I > > proceed or changes should I make in mdp file. > > Thanks > > > > -- > > Sonali Dhindwal > > > > > trjconv -o koko.pdb -dt 1000 -s -f -sep > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > 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 > sp...@xray.bmc.uu.se <http://mc/compose?to=sp...@xray.bmc.uu.se> > sp...@gromacs.org <http://mc/compose?to=sp...@gromacs.org> > http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > -- > gmx-users mailing list > gmx-users@gromacs.org<http://mc/compose?to=gmx-us...@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<http://mc/compose?to=gmx-users-requ...@gromacs.org> > . > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands
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