[gmx-users] RMSD from the average structure

[bipin singh]

Dear Sir,

Thanks for the useful insight.


On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> Average coordinates are problematic and not generally representative.
> Consider for instance the average coordinates of a methyl group connected
> to X. The rotation around the C-X bond causes the average positions of the
> hydrogens to line up. Consider using g_cluster to find representative
> structures from your trajectory.
>
> Erik
>
> On 26 Apr 2013, at 06:59, bipin singh <bipinelmat at gmail.com> wrote:
>
> > Thanks for your reply.
> > Actually I am interested to see how much structural deviation is
> occurring
> > in a protein during the simulation from its average position of atoms
> > rather than the initial position (crystal structure or starting
> structure).
> > The motivation of doing this analysis is the fact that in real solution
> > phase, a system may not be static and if we consider the time average
> > structure of a simulation to be the real representative of the structure
> in
> > solution phase rather than static crystal structure.
> >
> >
> >
> >
> >
> >
> >
> > On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
> >
> >> Hi Bipin Singh,
> >>
> >> That indeed gives you the RMSD against the average. Do think about it a
> bit
> >> more: do you want the average of the whole structure, or should you
> account
> >> for a phase of relaxation?
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >>
> >> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>>
> >>>
> >>> On 4/24/13 3:06 AM, bipin singh wrote:
> >>>
> >>>> Hi all,
> >>>>
> >>>> Please let me know whether this is the right way to calculate RMSD
> from
> >>>> the
> >>>> average structure from a simulation:
> >>>>
> >>>> g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
> >>>>
> >>>>
> >>>> average.pdb: is the pdb file produced using -ox option of g_rmsf.
> >>>>
> >>>>
> >>> You can calculate RMSD with respect to whatever structure you like, but
> >>> the interpretation and justification for doing so are up to you.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==============================**==========
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Research Scientist
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>>
> >>> ==============================**==========
> >>>
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> >>
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >> --
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> >
> >
> >
> > --
> > *-----------------------
> > Thanks and Regards,
> > Bipin Singh*
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-- 
*-----------------------
Thanks and Regards,
Bipin Singh*