On May 11, 2010, at 4:48 PM, Esteban Gabriel Vega Hissi wrote:
If we follow strictly the parameterization guides,
these are only guide lines ... no need to follow "strictly" :))
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.
This is only an idea!
Could be good. Need to be tested ... should not be too difficult.
Tell us about your results!!
Did I mention any result? I have none on urea :((
Best
Esteban
--
2010/5/11 XAvier Periole <x.peri...@rug.nl>
There is no Urea topology for Martini FF. Would be very interesting
to have one!
you need to look for some properties that you be able to reproduce.
have a look at the papers!
Typically you need to find logP (partitioning data) between different
media and and reproduce it using some Martini bead type ... and in
the case of Urea you might need to define a new type ...
XAvier.
On May 11, 2010, at 3:38 PM, Luca Mollica wrote:
Dear all,
I am looking for a urea topology for some CGMD simulations performed
with the MARTINI FF.
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.
Cheers,
Luca
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Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
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E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)
Telephone: +33.438783889
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