[gmx-users] CG-MD to study the conformational changes of proteins...

[Dariush Mohammadyani]

Hi Quyen,

Although Martini is a good CG force field for a system contains lipids and
proteins, it still needs some improvements to capture conformational
changes (especially large changes).
Is there any hybrid model available (and ready to use) for such a system?


Regards,
Dariush

On Mon, Dec 26, 2016 at 11:23 AM, Quyen V. Vu <vuqv.phys at gmail.com> wrote:

> Nikhil say:
>
> I would like to study the conformational study of proteins (Amyloid beta)
> in presence of lipid bilayers and other molecules. Can anyone tell me the
> possibility of Coarse-grained molecular dynamics for this study, since
> all-atom MD need more time and my system contains more atoms, so I'm
> thinking to go for CGMD.  in CG-MD can we do the same analysis as in
> All-atom MD.?
>
>
> You need to find a force field that support for protein coarse-grain model
>
> such as Martini: http://cgmartini.nl/
>
> to save simulation time you can you CG model or hybrid model( result
> better than CG model because a important region
>
> is treated as standard MD, less important region is use CG model
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