[gmx-users] Query- RMSD

[Tsjerk Wassenaar]

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
> > >
> > > --
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>
> --
> *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
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> posting!
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-- 
Tsjerk A. Wassenaar, Ph.D.