[gmx-users] change in secondary structure after npt equilibration
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 28 14:10:42 CET 2011
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>> 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>>/* wrote:
>
>
> From: Justin A. Lemkul <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>>
> 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>
> </mc/compose?to=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>>>
>
> >
>
> -- ========================================
>
> 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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> --
> ========================================
>
> 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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>
> --
> 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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