[gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <nehaphysics17 at gmail.com> wrote:

> Hi,
>
>
> Thank you for your prompt reply.
>
> By clustering analysis, are you talking about gmx cluster command?
>
> "over particular PC sub space"
>
> Could you please elaborate a bit?


Yea clustering analysis can interpret a lot datas about your complex
simulation.

Note:  I am not sure whether you Can perform gmx cluster over particular
sub space.

>
>
> Thanks a lot once again.
>
> Thanks,
> Neha
>
> On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <nehaphysics17 at gmail.com>
> > wrote:
> >
> > > Hi gromacs users,
> > >
> > > After MD simulation of protein-ligand complex for 5ns, can we view
> > protein
> > > folding?
> > >
> > > How to do it?
> > >
> > > I want to ascertain if there is any conformation change in protein
> where
> > > the ligand binds. Is it possible?
> > >
> > > We observe hydrogen bonds through molecular docking. Hence, I want to
> > make
> > > observation through MD simulation which is not obtained through
> docking.
> >
> >
> > You can perform Clustering analysis over particular PC sub space to
> measure
> > the structural changes.
> >
> > >
> > >
> > > Can someone help me regarding this?
> > >
> > > Thank you very much in advance.
> > >
> > > Thanks,
> > > Neha
> > > --
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> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*