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 ?? ...<br><br>
<div class="gmail_quote">On Fri, Jan 28, 2011 at 5:10 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im"><br><br>bharat gupta wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">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 ?? )<br>
<br></blockquote><br></div>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 :)<br>
<br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">On Fri, Jan 28, 2011 at 5:00 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> sonali dhindwal wrote:<br><br> Hi Justin,<br><br> I am writing in this correspondence, because I also had the same<br> query once that secondary structure changes after equilibration,<br> and you are right that visualisation programs are not always<br>
reliable.<br> You also mentioned this time that we should check wether<br> equilibration sufficiently converged all of the thermodynamic<br> observables. It will be very kind of you if you can throw some<br>
light in this regard that how these observables should be checked.<br><br><br> Presumably, you've chosen an ensemble (NVT, NPT, etc) that<br> represents some set of desirable conditions. You have to make sure<br>
that properties like temperature, pressure, density, energy, etc<br> have converged, otherwise the system is not yet equilibrated under<br> those conditions.<br><br> -Justin<br><br> Thanks and Regards<br><br>
-- Sonali Dhindwal<br><br> “Live as if you were to die tomorrow. Learn as if you were to<br> live forever.”<br><br><br> --- On *Fri, 28/1/11, Justin A. Lemkul /<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
</div> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>/* wrote:<br><br><br> From: Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>
<div class="im"><br> Subject: Re: [gmx-users] change in secondary structure after npt<br> equilibration<br> To: "Discussion list for GROMACS users"<br></div> <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>>
<div>
<div></div>
<div class="h5"><br> Date: Friday, 28 January, 2011, 5:53 PM<br><br><br><br><br> bharat gupta wrote:<br> > Hi,<br> ><br> ><br> > I am doing a simulation of a 230 amino acid protein for<br>
3ns ...<br> and I have completed the npt equilibration step .. After<br> retrieving<br> the structure from npt step and viewing it in pymol, reveals that<br> some portion of the beta strand got changed to a loop but when I<br>
visualized the same structure in VMD I found that nothing has<br> happened to the structure .. In order to confirm more ... I<br> generated the SS profile using dssp and I found that , the dssp<br>
shows E i.e. sheet for that region .. So what shall i do next ...<br> shall I continue with the production step or not ??<br> ><br><br> Visualization programs are not always reliable in what they show<br>
you, we've discussed that. Methods like DSSP and STRIDE are far<br> more trustworthy, and seem to indicate that your structure is<br> fine. What you should be much more concerned with at this<br>
point is whether<br> or not your equilibration sufficiently converged all of the<br> thermodynamic observables.<br><br> -Justin<br><br> > -- Bharat<br> > Ph.D. Candidate<br>
> Room No. : 7202A, 2nd Floor<br> > Biomolecular Engineering Laboratory<br> > Division of Chemical Engineering and Polymer Science<br> > Pusan National University<br> > Busan -609735<br>
> South Korea<br> > Lab phone no. - +82-51-510-3680, +82-51-583-8343<br> ><br> > Mobile no. - 010-5818-3680<br></div></div> > E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a> <mailto:<a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a>><br>
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<div class="im"><br><br> ><br><br> -- ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> MILES-IGERT Trainee<br>
Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080
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Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<br>Mobile no. - 010-5818-3680<br>
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<div class="im"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343
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