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
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