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

[bharat gupta]

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 ?? )

On Fri, Jan 28, 2011 at 5:00 AM, Justin A. Lemkul <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>/* 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.
>>
>>    -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 </mc/compose?to=monu46010 at yahoo.com>
>>    <mailto:monu46010 at yahoo.com </mc/compose?to=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
>>    </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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>
>>
>>
> --
> ========================================
>
> 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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110128/8267ac72/attachment.html>