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

Luca Mollica luca.mollica at ibs.fr
Tue May 11 17:21:27 CEST 2010

On 05/11/2010 04:57 PM, XAvier Periole wrote:
> 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" :))

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 ... :)

>> 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.

I agree with you: this is what I had in mind.
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
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
field, as far as I have understood) but rather to observe mesoscale 
dynamics of "already" unfolded peptides in solution.
At the moment I have a good topology for FGMD that has been adapted from 
this paper :

A Kirkwood-Buff Derived Force Field for Mixtures of Urea and Water Source
/The Journal Of Physical Chemistry B/ Volume: 107 Issue: 16 (2003-01-01) 
p. 3891-3898.

that has recently be used in this paper

Equilibrium study of protein denaturation by urea.
/The Journal of the American chemical Society/, 2010 Feb 24;132(7): 2338-44.

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,
once implemented ... the test can be hard, the implementation, actually, 
is almost straightforward.

>> Tell us about your results!!
> Did I mention any result? I have none on urea :((

I presume Esteban inteded my ones ... I read this expectation as a "good 
luck" and "enjoy topology making".

In case we will keep in touch.


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