<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>A few notes:</div><div>- the original method (Kumar-JCC-1992) that inspired wham was actually </div><div>developed to mix different temperature simulations. It is however not clear </div><div>for the type of system you are simulating how much a 500K simulation </div><div>would be useful to improve the sampling at 300 K or so. The reason is </div><div>that the enthalpy difference between the two systems is so high that the </div><div>probability that a conformation from a 500K simulation would contribute</div><div>to sampling at 300K is really low. It would much more efficient for systems </div><div>with implicit solvent for which the energy of the system does not vary so </div><div>much with the temperature. One could look at Chodera-JCTC-2007 </div><div>and ref therein for a few examples.</div><div>- I would think that a REMD simulation would be more useful. No need to</div><div>run 30 replicas to very hight temperature! A bilayer at 500K might get funny.</div><div><br></div><div>- Martini force field for flexible regions of protein should not be trusted ... or</div><div>really interpreted with a lot of reserve. The "coil" definition is simply something</div><div>flexible with absolutely no guaranty that it could be representing some thing </div><div>even close to reality, which we have only an approximate idea of what it is! </div><div><br></div><div>- A peptide in a bilayer has a very high chance to get into a helical conformation.</div><div>Do you think it is reasonable to keep it "flexible"? </div><div><br></div><div>- As noted by Justin and Chris, you definitely have a problem of convergence ... </div><div>I am not sure how many "converged" examples of PMFs of peptide crossing a</div><div>bilayer are out in the literature (Justin?) but from our experience with Martini </div><div>it does take an awful lot of time to really get convergence. For you system I </div><div>would expect at least a microsecond for the windows where sampling is an </div><div>issue. As an example, we saw significant differences on a PMF between two </div><div>simple helices up to 8 us ... and no charges were involved.</div><div><br></div><div>This might be a lot pessimistic but you should not get fooled by a CG model.</div><div>Martini is really good for a lot of things but other things should really but be</div><div>looked at carefully. </div><div><br></div><div>XAvier.</div><div><br></div><div><div>On Feb 22, 2011, at 9:12 AM, Jianguo Li wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><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-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; font-size: medium; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sorry I forgot to attach my mdp files. <br><br>Here is the mdp file for pulling simulaition:<br>-------------------------------------------------------------------------<br></div></div></div></span></blockquote></div><div><div><br></div></div></body></html>