Thanks for ur kind reply Justin ...<div><br></div><div>I also searched the gmx userlist regarding the same query and I found out that It was mentioned to repeat the simulation again with a different force field .. but I don't know about the energy minimization parameters as I am following ur lysozyme tutorial for that .. I will get back to u get if I get the same type of structural changes with this force field... </div>
<div><br></div><div>Also I would like to mention one more thing .. as I did the simulation of crystal str of GFP with the same parameters which I used for the variant of GFP .. In case of the crystal str. simulation result, it seems to be perfectly fine and there is no change in the secondary structure also ... So, if I am not wrong then there is some problem with the variant structure that I have modeled ??.. Actually the variant of GFP that I have modeled has one loop (of 4 amino acid in original str) replaced with an another loop of 9 residues length ... CAn this be the reason ??</div>
<div><br></div><div>Regarding the simulation time I want to ask ... what is the minimum or the optimal time the structure should be simulated for such analysis as I have read many paper published in big journals doing simulation only for 1ns (in that case I am doing for 3 ns)... pls comment<br>
<br><div class="gmail_quote">On Wed, Feb 2, 2011 at 3:34 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I think I have asked this question earlier in the forum .. that during my 3ns simulation of a 230 amino acid proteins some portion of 2 beta strands got converted to loop/random coil, after visualizing in VMD. I checked the DSSP profile also .. and as per the DSSP results it's coil in that region .. can anybody tell me where can the error be as I have been checking my structure right from the minimization step till npt equilibration and its was fine ... this has happened only after simulation ... pls help ?? <br>
</blockquote>
<br></div>
The comments I made last week still stand:<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html</a><br>
<br>
You're basing your conclusions on a 3-ns simulation, which I would say is far too short to obtain any meaningful data for such a system.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
-- <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>
Mobile no. - 010-5818-3680<br></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>
<br>
</blockquote>
<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>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></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<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>
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