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

[Esteban Gabriel Vega Hissi]

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.
This is only an idea! Tell us about your results!!

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
>>
>>
>> --
>>
>>
>> Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack
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