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

[sonali dhindwal]

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 <tsjerkw at gmail.com> wrote:

From: Tsjerk Wassenaar <tsjerkw at gmail.com>
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, 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 <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    spoel at 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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