Thanks
--
Sonali Dhindwal
--- On *Fri, 16/7/10, Oliver Grant /<olymacfoo...@gmail.com>/* wrote:
From: Oliver Grant <olymacfoo...@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, 3:36 PM
0ns, 1ns, 2ns and 3ns gives four files.
On 16 July 2010 10:47, sonali dhindwal <sonali11dhind...@yahoo.co.in
</mc/compose?to=sonali11dhind...@yahoo.co.in>> wrote:
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
</mc/compose?to=tsje...@gmail.com>>/* wrote:
From: Tsjerk Wassenaar <tsje...@gmail.com
</mc/compose?to=tsje...@gmail.com>>
Subject: Re: [gmx-users] to visualise protein conformation
after every 1ns
To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org </mc/compose?to=gmx-us...@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
<http://mc/compose?to=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
<http://mc/compose?to=sp...@xray.bmc.uu.se>>/* wrote:
From: David van der Spoel <sp...@xray.bmc.uu.se
<http://mc/compose?to=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
<http://mc/compose?to=gmx-us...@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
<http://mc/compose?to=sp...@xray.bmc.uu.se>
sp...@gromacs.org
<http://mc/compose?to=sp...@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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