You can try rmsd and gyrate plot to see the changes in your complex. It On Dec 19, 2017 2:22 PM, "RAHUL SURESH" <drrahulsur...@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 <nehaphysic...@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 <drrahulsur...@gmail.com> > > wrote: > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <nehaphysic...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.