[gmx-users] change in secondary structure after npt equilibration
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 28 14:39:19 CET 2011
bharat gupta wrote:
> I searched the user list .. I am not able to find how to apprach this
> problem .. I want to check whether water is entering the protein and
> interacting with chromophore or not ?? ...
>
There's not going to be a how-to for everything you might want to do. The best
place to start is spend a while reading g_select -select "help examples" and
doing some experimentation. There are a few examples in the archive of what
people have done, but not specifically what you're looking to do. In any case,
the syntax and logic should be beneficial.
For future posts, specific questions will often get better, more specific
answers. If you try to use g_select and it doesn't work, post what you tried
and what it gave you, and why that's not correct. You'll get better advice that
way.
-Justin
> On Fri, Jan 28, 2011 at 5:10 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> bharat gupta wrote:
>
> Thanks for the advice ... I have checked all the equilibration
> graphs and they have converged well... I want to know one more
> thing about the anaylsis of simulation result.... I want to know
> whether the water molecules are entering in the protein molecule
> or not and if so how to track down those specific water
> molecules .. ( since I am simulating a GFP which is well
> protected from water and I have made some changes in the
> structure of GFP and then simulating it to see how this leads to
> change in protein structure ?? )
>
>
> Watching the trajectory is the first step. There may be ways to
> quantify these water molecules, using e.g. g_select or perhaps
> trjorder, but I can't say that I actually know how to do that. I've
> never had to try :)
>
> -Justin
>
> On Fri, Jan 28, 2011 at 5:00 AM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> sonali dhindwal wrote:
>
> Hi Justin,
>
> I am writing in this correspondence, because I also had
> the same
> query once that secondary structure changes after
> equilibration,
> and you are right that visualisation programs are not always
> reliable.
> You also mentioned this time that we should check wether
> equilibration sufficiently converged all of the thermodynamic
> observables. It will be very kind of you if you can throw
> some
> light in this regard that how these observables should be
> checked.
>
>
> Presumably, you've chosen an ensemble (NVT, NPT, etc) that
> represents some set of desirable conditions. You have to
> make sure
> that properties like temperature, pressure, density, energy, etc
> have converged, otherwise the system is not yet equilibrated
> under
> those conditions.
>
> -Justin
>
> Thanks and Regards
>
> -- Sonali Dhindwal
>
> “Live as if you were to die tomorrow. Learn as if you were to
> live forever.”
>
>
> --- On *Fri, 28/1/11, Justin A. Lemkul /<jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>/* wrote:
>
>
> From: Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>>
>
> Subject: Re: [gmx-users] change in secondary structure
> after npt
> equilibration
> To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>
>
> Date: Friday, 28 January, 2011, 5:53 PM
>
>
>
>
> bharat gupta wrote:
> > Hi,
> >
> >
> > I am doing a simulation of a 230 amino acid protein for
> 3ns ...
> and I have completed the npt equilibration step .. After
> retrieving
> the structure from npt step and viewing it in pymol,
> reveals that
> some portion of the beta strand got changed to a loop
> but when I
> visualized the same structure in VMD I found that
> nothing has
> happened to the structure .. In order to confirm more
> ... I
> generated the SS profile using dssp and I found that ,
> the dssp
> shows E i.e. sheet for that region .. So what shall i
> do next ...
> shall I continue with the production step or not ??
> >
>
> Visualization programs are not always reliable in what
> they show
> you, we've discussed that. Methods like DSSP and
> STRIDE are far
> more trustworthy, and seem to indicate that your
> structure is
> fine. What you should be much more concerned with at this
> point is whether
> or not your equilibration sufficiently converged all
> of the
> thermodynamic observables.
>
> -Justin
>
> > -- Bharat
> > Ph.D. Candidate
> > Room No. : 7202A, 2nd Floor
> > Biomolecular Engineering Laboratory
> > Division of Chemical Engineering and Polymer Science
> > Pusan National University
> > Busan -609735
> > South Korea
> > Lab phone no. - +82-51-510-3680, +82-51-583-8343
> >
> > Mobile no. - 010-5818-3680
> > E-mail : monu46010 at yahoo.com
> <mailto:monu46010 at yahoo.com> <mailto:monu46010 at yahoo.com
> <mailto:monu46010 at yahoo.com>>
> </mc/compose?to=monu46010 at yahoo.com
> <mailto:monu46010 at yahoo.com> <mailto:monu46010 at yahoo.com
> <mailto:monu46010 at yahoo.com>>>
> <mailto:monu46010 at yahoo.com
> <mailto:monu46010 at yahoo.com> <mailto:monu46010 at yahoo.com
> <mailto:monu46010 at yahoo.com>>
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> <mailto:monu46010 at yahoo.com> <mailto:monu46010 at yahoo.com
> <mailto:monu46010 at yahoo.com>>>>
>
>
> >
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> |
> (540) 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
> <mailto:monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>>
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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> gmx-users mailing list gmx-users at gromacs.org
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>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>
--
========================================
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
========================================
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