<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On May 11, 2010, at 4:48 PM, Esteban Gabriel Vega Hissi wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">If we follow strictly the parameterization guides, </blockquote>these are only guide lines ... no need to follow "strictly" :))<br><blockquote type="cite">Urea has to be mapped to only one CG bead (because of reduction from 4 to 1), but I believe that this would not be able to represent properties of the molecule. Instead I would use a 2 beads model or try something like it has been done with water, i.e., more than one urea molecule to 1 or 2 beads.<br></blockquote><blockquote type="cite">This is only an idea! </blockquote>Could be good. Need to be tested ... should not be too difficult.<br><blockquote type="cite">Tell us about your results!!<br></blockquote>Did I mention any result? I have none on urea :((<br><blockquote type="cite"><br>Best<br><br>Esteban<br>--<br><br><div class="gmail_quote"> 2010/5/11 XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> There is no Urea topology for Martini FF. Would be very interesting to have one!<br> <br> you need to look for some properties that you be able to reproduce.<br> have a look at the papers!<br> <br> Typically you need to find logP (partitioning data) between different<br> media and and reproduce it using some Martini bead type ... and in<br> the case of Urea you might need to define a new type ...<br> <br> XAvier.<div><div></div><div class="h5"><br> <br> On May 11, 2010, at 3:38 PM, Luca Mollica wrote:<br> <br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Dear all,<br> I am looking for a urea topology for some CGMD simulations performed with the MARTINI FF.<br> Actually I am planning to design it on my own, but in case at least a "source of inspiration" (I have found no papers about the issue) would be appreciated.<br> Cheers,<br> <br> Luca<br> <br> <br> <br> -- <br> <br> ........................................................<br> <br> --<br> <br> <br> <br> Luca Mollica<br> Protein Dynamics and Flexibility by NMR<br> Institut de Biologie Structurale<br> 41 Rue Jules Horowitz<br> Grenoble<br> 38027<br> France<br> <br> E-mail: <a href="mailto:luca.mollica@ibs.fr" target="_blank">luca.mollica@ibs.fr</a> (<a href="mailto:lucamollica@gmail.com" target="_blank">lucamollica@gmail.com</a>)<br> <br> Telephone: +33.438783889<br> <br> <br> --<br> <br> <br> Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of cigarettes, it's dark, and we're wearing sunglasses.<br> Jake: Hit it.<br> <br> (The Blues Brothers)<br> <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/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </div></div></blockquote></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/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/mailing_lists/users.php</blockquote></div><br></body></html>