If we follow strictly the parameterization guides, 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>This is only an idea! Tell us about your results!!<br><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. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
<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></div></div>
Please don't post (un)subscribe requests to the list. Use thewww interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<div><div></div><div class="h5">
<br>
Can't post? 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>