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> 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 sp...@gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- 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 -- 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 -----Inline Attachment Follows----- -- 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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