[gmx-users] RMSD from the average structure

[bipin singh]

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*