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<font face="Times New Roman, Times, serif">On 05/11/2010 04:57 PM,
XAvier Periole wrote:</font>
<blockquote cite="mid:E17401F2-3DC2-4BF1-AB0B-9785FCC9C7B0@rug.nl"
type="cite"><font face="Times New Roman, Times, serif"><br>
</font>
<div>
<div><font face="Times New Roman, Times, serif">On May 11, 2010, at
4:48 PM, Esteban Gabriel Vega Hissi wrote:</font></div>
<font face="Times New Roman, Times, serif"><br
class="Apple-interchange-newline">
</font>
<blockquote type="cite"><font face="Times New Roman, Times, serif">If
we follow strictly the parameterization guides, </font></blockquote>
<font face="Times New Roman, Times, serif">these are only guide lines
... no need to follow "strictly" :))<br>
</font></div>
</blockquote>
<font face="Times New Roman, Times, serif"><br>
Actually this was the problem: CG seems easy because of a reduced
number of points, however getting into the thing (I have experience
only in FG MD) it's easily realizable that misleading representations
of molecules can be obtained quite straightforwardly ... :)<br>
<br>
<br>
</font>
<blockquote cite="mid:E17401F2-3DC2-4BF1-AB0B-9785FCC9C7B0@rug.nl"
type="cite">
<div>
<blockquote type="cite"><font face="Times New Roman, Times, serif">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>
</font></blockquote>
<blockquote type="cite"><font face="Times New Roman, Times, serif">This
is only an idea! </font></blockquote>
<font face="Times New Roman, Times, serif">Could be good. Need to be
tested ... should not be too difficult.<br>
</font></div>
</blockquote>
<font face="Times New Roman, Times, serif"><br>
I agree with you: this is what I had in mind.<br>
Honestly speaking, I am looking for a cosolvent molecule for simulating
a suitable environment unfolded proteins, that are the systems I am
currently working on also with the help of <br>
experimental techniques (like SAXS, SANS, NMR or fluorescence). Hence,
I am not interested in unfolding anything (the usage of Martini for
protein unfolding is not yet an estabilished <br>
field, as far as I have understood) but rather to observe mesoscale
dynamics of "already" unfolded peptides in solution.<br>
At the moment I have a good topology for FGMD that has been adapted
from this paper :<br>
<br>
<span id="ctl00_ContentPlaceHolder1__citationArea__titleLabel"
class="titleLabel"></span><span class="style2"><span
id="ctl00_ContentPlaceHolder1__citationArea__titleDisplay"
class="titleDisplay">A Kirkwood-Buff Derived Force Field for Mixtures
of Urea and Water</span> </span><span
id="ctl00_ContentPlaceHolder1__citationArea__sourceLabel"
class="sourceLabel">Source<br>
</span><span id="ctl00_ContentPlaceHolder1__citationArea__sourceDisplay"
class="sourceDisplay"><i>The Journal Of Physical Chemistry B</i>
Volume: 107 Issue: 16 (2003-01-01) p. 3891-3898. </span><br>
<br>
that has recently be used in this paper <br>
</font> <br>
<font face="Times New Roman, Times, serif">Equilibrium study of protein
denaturation by urea.</font>
<br>
<font face="Times New Roman, Times, serif"><i>The Journal of the
American chemical Society</i>, 2010 Feb 24;132(7): 2338-44.<br>
</font><br>
<font face="Times New Roman, Times, serif"><br>
and that I have implemented adapting the existing urea FFAMBER
topology. I think the that same experiments reported in the
aforementioned paper could be used as a benchmark for CGMD, <br>
once implemented ... the test can be hard, the implementation,
actually, is almost straightforward. <br>
<br>
<br>
</font>
<blockquote cite="mid:E17401F2-3DC2-4BF1-AB0B-9785FCC9C7B0@rug.nl"
type="cite">
<div>
<blockquote type="cite"><font face="Times New Roman, Times, serif">Tell
us about your results!!<br>
</font></blockquote>
<font face="Times New Roman, Times, serif">Did I mention any result?
I have none on urea :((<br>
</font></div>
</blockquote>
<font face="Times New Roman, Times, serif"><br>
I presume Esteban inteded my ones ... I read this expectation as a
"good luck" and "enjoy topology making".<br>
:D<br>
<br>
In case we will keep in touch.<br>
Cheers<br>
<br>
Luca<br>
<br>
<br>
</font><br>
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