[gmx-users] Query- RMSD

[Priya Das]

Thank you All.

On Tue, Apr 7, 2015 at 5:55 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Priya,
>
> You only mentioned that you did 10ns of simulation of a protein/ligand
> system and calculated the RMSD. There is not that much to comment on. If
> you want more elaborate comments, you need to ask more elaborate questions,
> give more background, explain why you would expect 10ns to be enough, and
> put the plot somewhere for us to see.
>
> That said, 10 ns is not enough to reach convergence of a system with a
> protein, period. You will need much more.
>
> Cheers,
>
> Tsjerk
>
> On Tue, Apr 7, 2015 at 2:20 PM, Priya Das <priyadas001 at gmail.com> wrote:
>
> > Can you comment more on it?
> > Should i increase the time for simulation?
> >
> > On Tue, Apr 7, 2015 at 4:16 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >
> > > No.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > > On Apr 7, 2015 12:16 PM, "Priya Das" <priyadas001 at gmail.com> wrote:
> > >
> > > > Dear all,
> > > >
> > > > For checking ligand interactions with protein , i generated a RMSD
> plot
> > > for
> > > > ligand. The simulations were done for 10 ns. Has the system
> converged?
> > > >
> > > > ​
> > > >
> > > > --
> > > > *Let us all join hands to save our " Mother Earth"*
> > > >
> > ------------------------------------------------------------------------
> > > > Regards,
> > > > Priya Das
> > > > Research Scholar
> > > > Dept. of Computational Biology and Bioinformatics,
> > > > University of Kerala
> > > >
> > > > --
> > > > 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.
> >
> >
> >
> >
> > --
> > *Let us all join hands to save our " Mother Earth"*
> > ------------------------------------------------------------------------
> > Regards,
> > Priya Das
> > Research Scholar
> > Dept. of Computational Biology and Bioinformatics,
> > University of Kerala
> > --
> > 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.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> 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.
>



-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala