[gmx-users] to visualise protein conformation after every 1ns

sonali dhindwal sonali11dhindwal at yahoo.co.in
Fri Jul 16 09:58:35 CEST 2010

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

Am I doing it correct ?

Sonali Dhindwal

--- On Fri, 16/7/10, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] to visualise protein conformation after every 1ns
To: "Discussion list for GROMACS users" <gmx-users at 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 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
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