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