<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>As Justin pointed out, there is a vast literature on this topic, you need to ask yourself what you seek, and look at many review articles to find some reasonable starting points for you own needs and designs. Beyond that, it's a lot of hard work... </div><br><div><div>On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Thanks for your advice... Could you please refer me some papers regarding this ....<br><br><div class="gmail_quote">On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi <span dir="ltr"><<a href="mailto:ksr@chemistry.umass.edu">ksr@chemistry.umass.edu</a>></span> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">No, there is no way to use such data to determine the folding rate of the intact protein. If you used a fragment approach you could potentially (read lots of papers on REMD) isolate nucleation sites, but minus the tertiary interaction scheme you could not tell a compelling story. Now, if you want to find nucleation sites and see if there are spatially proximal sites and simulate them together... You might begin to tell a story.<br> <br> Ken<div><div class="h5"><br> <br> On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:<br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br> <br> bharat gupta wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Thanks for your reply. I want to whether does it make any sense or is it possible to simulate fragments of proteins and find their folding rate and then correlate it to folding rate of whole protein ??<br> </blockquote> <br> Simulating arbitrary parts of a protein may or may not produce any relevant information, likely the latter. Independently folding domains might be simulated in isolation, but if there is a chance that the peptide sequences have any effect on neighboring residues or even more distal sites, you'll never produce anything useful.<br> <br> -Justin<br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> On Sat, Dec 31, 2011 at 8:00 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> bharat gupta wrote:<br> Hi,<br> I want to know whether it's possible to calculate the folding<br> rate of 20 residue peptide folding into a beta-hairpin using<br> gromacs ??<br> Anything is possible ;) But seriously, there is existing literature<br> on such topics, I suspect you can find methodology that will suit<br> your needs.<br> -Justin<br> -- ==============================<u></u>__==========<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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>__<a href="http://vt.edu/Pages/Personal/justin" target="_blank"><u></u>vt.edu/Pages/Personal/justin</a><br> <<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a>><br> ==============================<u></u>__==========<br> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br> <a href="http://lists.gromacs.org/__mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/__<u></u>mailman/listinfo/gmx-users</a><br> <<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a>><br> Please search the archive at<br> <a href="http://www.gromacs.org/__Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists/Search</a><br> <<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a>> before posting!<br> Please don't post (un)subscribe requests to the list. 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Read <a href="http://www.gromacs.org/__Support/Mailing_Lists" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists</a><br> <<a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a>><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> Mobile no. - 010-5818-3680<br> 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> </blockquote> <br> -- <br> ==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br> <br> ==============================<u></u>==========<br> -- <br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br> Please don't post (un)subscribe requests to the list. 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Use thewww interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<div class="HOEnZb"><div class="h5"> <br> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br> </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<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></body></html>