[gmx-users] change in secondary structure after npt equilibration
bharat gupta
bharat.85.monu at gmail.com
Fri Jan 28 14:34:58 CET 2011
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 ?? ...
On Fri, Jan 28, 2011 at 5:10 AM, Justin A. Lemkul <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>> 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
>>
>> ========================================
>> -- 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at
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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
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