<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Is this a real gromacs-user question? <div><br></div><div>Have your tried to contact the MArtini developers? </div><div><br></div><div>As a matter of fact some of them have prepared a new MARTINI</div><div>web-site where a discussion forum will be on. </div><div><br></div><div>To answer your question: using MARTINI for the unfolding </div><div>mechanism of proteins would be very challenging to put it nice. </div><div>It is not "AT ALL" made for that! </div><div><br></div><div>The use of Go-model has be tested (for other purposes) and </div><div>it would be at least as "bad" as using an all atom FF. No need </div><div>to use a CG model with Go-models, atomistic are fast enough.</div><div>Well that is my current opinion.</div><div><br><div><div>On Dec 16, 2009, at 11:36 AM, rasoul nasiri 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-size: medium; 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; -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>Dear GMX users,<br>Hi<br><br>I'm working on denaturation of proteins with MARTINI CGFF by Gromacs suit.<br>according to this paper (J. Chem. Theory and Comput. 2008, 4, 819–834) I undestand there is a limitation for modeling of folding and unfolding with MARITI CGFF for systems in which the folding and unfolding of secondary<span class="Apple-converted-space"> </span>structures are playing a substantial role are therefore not suitable for modeling with current CG force field.<br>since I perform CGMD simulation on tertiary structure, is there this limitation on my system or no?<br>If your question is positive, Is there an improved version of MARTINI CGFF for doing it?<br>Can I use Gō model for resolve of this problem?<br>What is your idea about this problem?<br><br>I'm looking forward to hearing from you about this matter!<br><br>Beast Regards<br>Rasoul<span class="Apple-converted-space"> </span><br>--<span class="Apple-converted-space"> </span><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<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br></div></body></html>