Victor,
I appreciate your answer. Basically, one goal of this investigation
is to reproduce some of the amphiphilic behavior of a molecule that we have
synthesize here in the lab. We would like to simulate the transition from a
aqueous environment to an apolar one and the conformation change of our
molecule to better understand the mechanism of these types of molecules. The
first idea was to use MARTINI to do this, so we tried using this tool, and we
get some results but we would like to construct a more accurate coarse grained
representation of the studied molecule.
I will se the literature that you have propose. Thanks for your help,
Marc-André
Le 2011-09-01 à 12:02, Victor Ruehle a écrit :
> Dear Marcc-André,
>
> are you now just asking about the technical aspect, or about the
> method itself? If the latter, there is no clear answer to your
> problem. There are various methods available. The first question you
> should ask yourself is what kind of properties you want to reproduce
> in with your coarse-grained model.
>
> Most methods implemented in VOTCA are structure based approaches (or
> closely related to it) and therefore will most probably do wrong on
> thermodynamics. You can e.g. check the VOTCA references
> (http://www.votca.org/citations), there are also lot's of references
> given in the papers for more details on the method or links to other
> methods. That's still an incomplete list, but might be a good point to
> start with.
>
> If you want to act on the rdfs, I would start with IBI (see section in
> the manual). Otherwise, also force-matching or a hybrid approach might
> be worth a try. It's not yet officially supported in VOTCA, but
> depending on your system, it might be worth to have a look at what the
> MARTINI force field people did.
>
> Don't hesitate to ask any further questions, but providing some more
> details might help...
>
> Best,
> Victor
>
> 2011/9/1 Marc-André Dubois <[email protected]>:
>> Hi all,
>> I tried to follow the tutorials that you provide on your website.
>> Coarse-grained models are not actually the biggest concern of my group, so I
>> have to start from the basis. As I actually understand the thing, I have to:
>>
>> 1. constructs an atomistic representation of the system, which will give to
>> you data to construct the coarse grained representation.
>> 2. runs a molecular dynamic at the atomistic scale
>> 3. obtains the radial distribution function for each of your CG beads
>>
>> From step 1 to step 3, I think that everything works fine. From these steps,
>> how it is possible to find the actual interaction potentials of the CG beads
>> to constructs a forcefield that GROMACS will understand? I am sorry that
>> this question would seems trivial, but as I previously said, I am not
>> familiar with these kind of experiments. Thank you,
>>
>> Marc-André Dubois
>>
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