[gmx-users] urea topology for MARTINI (CGMD)

[XAvier Periole]

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.periole at 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
>
>
>
> -- 
>
> ........................................................
>
> --
>
>
>
> Luca Mollica
> Protein Dynamics and Flexibility by NMR
> Institut de Biologie Structurale
> 41 Rue Jules Horowitz
> Grenoble
> 38027
> France
>
> E-mail: luca.mollica at ibs.fr (lucamollica at gmail.com)
>
> Telephone: +33.438783889
>
>
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