Hi guys,
Is there a way to obtain The Lennard-Jones potential energy
terms for the interaction between 2 CG beads from the radial distribution
function? Thank you,
Marc-André
Le 2011-09-01 à 12:21, Marc-André Dubois a écrit :
> 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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>>>
>>
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>
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