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

[Oliver Grant]

0ns, 1ns, 2ns and 3ns gives four files.

On 16 July 2010 10:47, sonali dhindwal <sonali11dhindwal at 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 <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<http://mc/compose?to=sonali11dhindwal@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<http://mc/compose?to=spoel@xray.bmc.uu.se>
>> >* wrote:
>>
>>
>> From: David van der Spoel <spoel at xray.bmc.uu.se<http://mc/compose?to=spoel@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<http://mc/compose?to=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
>> 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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