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

[Tsjerk Wassenaar]

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 <
sonali11dhindwal at 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 <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.
> ________________________________________________________________________
> 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
> spoel at xray.bmc.uu.se <http://mc/compose?to=spoel@xray.bmc.uu.se>
> spoel at gromacs.org <http://mc/compose?to=spoel@gromacs.org>
> http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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-- 
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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