[gmx-users] change in secondary structure after npt equilibration

sonali dhindwal sonali11dhindwal at yahoo.co.in
Fri Jan 28 13:49:20 CET 2011

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.

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> wrote:

From: Justin A. Lemkul <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>
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.


> -- 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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