<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Bharat, <div><br></div><div>20 residue peptides in general don't fold, they inhabit a conformational space. Can you determine the fraction of time spent in a near native (as defined by you) conformation under given conditions to within the ability of the force field, yes, you can. To calculate a true rate of folding, if you were studying, say, the trp cage protein (20 AA, defined tertiary structure), you'd have to start with a primarily beta or helix chain (use a primary sequence secondary structure predictor to assign starting conformations) as would be expected to emerge from the ribosome, simulate until a native-like conformation was formed, and repeat many times until a statistically reasonable answer was approached, and even then, for something that small, I'd bet it spends a fair amount of time in non-native conformations.</div><div><br></div><div>Many times.</div><div><br></div><div>Ken</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; 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-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Dr. K.S. Rotondi</div><div>Departments of Chemistry, Biochemistry and Molecular Biology</div><div>The University of Massachusetts - Amherst</div><div>Amherst, MA 01003</div><div><br class="khtml-block-placeholder"></div><div>"If there's a solution, why worry?, If there's no solution, why worry?"</div><div><span class="Apple-tab-span" style="white-space: pre; "><span class="Apple-style-span" style="white-space: pre; "><span class="Apple-style-span" style="white-space: pre; "> </span></span></span>His Holiness, the Dalai Llama</div><div><br class="khtml-block-placeholder"></div></span></span></div></span></div></span></div></span></div></span></div></span></div></span><span class="Apple-style-span" style="font-size: 12px;"><br class="Apple-interchange-newline"></span> </div><br><div><div>On Dec 30, 2011, at 5:39 PM, bharat gupta wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br><br>I want to know whether it's possible to calculate the folding rate of 20 residue peptide folding into a beta-hairpin using gromacs ??<br clear="all"><br>-- <br>Bharat<br><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></div></body></html>