0ns, 1ns, 2ns and 3ns gives four files. On 16 July 2010 10:47, sonali dhindwal <sonali11dhind...@yahoo.co.in> wrote:
> Thanks Tsjerk, > I was confused, that why 3 files are generated as output. I will check it. > I appreciate what you said, I will read more. > Regards > > -- > Sonali Dhindwal > > > --- On *Fri, 16/7/10, Tsjerk Wassenaar <tsje...@gmail.com>* wrote: > > > From: Tsjerk Wassenaar <tsje...@gmail.com> > > 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, 1:43 PM > > 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, > > > > On Fri, Jul 16, 2010 at 9:58 AM, sonali dhindwal < > sonali11dhind...@yahoo.co.in<http://mc/compose?to=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<http://mc/compose?to=sp...@xray.bmc.uu.se> >> >* wrote: >> >> >> From: David van der Spoel >> <sp...@xray.bmc.uu.se<http://mc/compose?to=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<http://mc/compose?to=gmx-us...@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://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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > > -----Inline Attachment Follows----- > > > -- > 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 >
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