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

[Shanmuga Priya V.G]

Dear Gromacs Users,
I have a insilico model of Mycobacterium cell wall  (surface) protein
which has no transmembrane helices.Which Gromacs tutorials should I
follow for MD studies to know about its conformational stability and
latter for protein - ligand studies. Kindly guide me

Thanking you

with regards
V.G.Shanmuga Priya

On Mon, Dec 26, 2016 at 11:06 PM, Dariush Mohammadyani <
d.mohammadyani at gmail.com> wrote:

> 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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