[gmx-users] PROTEIN FOLDING

[Aman Deep]

You can try rmsd and gyrate plot to see the changes in your complex. It
On Dec 19, 2017 2:22 PM, "RAHUL SURESH" <drrahulsuresh at gmail.com> wrote:

> Also you must know, a lot analysis are available over the entire manual of
> Gromacs where all cannot be performed. Gromacs always provide you all
> necessary analysis but to choose which one is always your choice that suits
> your simulation purpose.
>
>
> 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?
> >
> > 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
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>