[gmx-users] to visualise protein conformation after every 1ns
Justin A. Lemkul
jalemkul at vt.edu
Fri Jul 16 14:09:47 CEST 2010
sonali dhindwal wrote:
> ok, 4 files, my mistake, I checked all the files and they have RMSD
> among themselves of 2-3 Angstrom, can you please explain it why it is so ?
Why wouldn't they? Are you expecting them to be the same?
You won't get much in the way of an explanation for most questions like these.
Only you know the system you're studying, how flexible it might be, etc.
-Justin
> Thanks
>
> --
> Sonali Dhindwal
>
>
> --- On *Fri, 16/7/10, Oliver Grant /<olymacfoogal at gmail.com>/* wrote:
>
>
> From: Oliver Grant <olymacfoogal 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, 3:36 PM
>
> 0ns, 1ns, 2ns and 3ns gives four files.
>
> On 16 July 2010 10:47, sonali dhindwal <sonali11dhindwal at yahoo.co.in
> </mc/compose?to=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
> </mc/compose?to=tsjerkw at gmail.com>>/* wrote:
>
>
> From: Tsjerk Wassenaar <tsjerkw at gmail.com
> </mc/compose?to=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 </mc/compose?to=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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> --
> gmx-users mailing list gmx-users at gromacs.org
> <http://mc/compose?to=gmx-users@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the
> list. Use the
> www interface or send it to
> gmx-users-request at gromacs.org
> <http://mc/compose?to=gmx-users-request@gromacs.org>.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <http://mc/compose?to=gmx-users@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list.
> Use the
> www interface or send it to
> gmx-users-request at gromacs.org
> <http://mc/compose?to=gmx-users-request@gromacs.org>.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
>
> -----Inline Attachment Follows-----
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <http://mc/compose?to=gmx-users@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <http://mc/compose?to=gmx-users-request@gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> </mc/compose?to=gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> -----Inline Attachment Follows-----
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> </mc/compose?to=gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> </mc/compose?to=gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list