=?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20=BB=D8=B8=B4=A3=BA=20Re:=20[gmx-use?= =?gb2312?q?rs]=20r.m.s.i.p?=

[xi zhao]

Dear Tsjerk :
  Thank you very much!

Tsjerk Wassenaar <tsjerkw at gmail.com> дµÀ£º
  Hi Xi Zhao,

Please find attached a .csh script you can use to calculate the rmsip.
The script is of the hand of Isabella Daidone, now in Heidelberg.

Note that for a set of 'equal' simulations there is a spread in the
values you obtain for the RMSIP (i.e. it's not an absolute measure of
equality unless you have full convergence of your simulations). If you
want to use the RMSIP to really compare simulations check our paper in
JCC 27 p. 316 (2006).

Cheers,

Tsjerk

On 9/18/06, xi zhao wrote:
> Based on the essential dynamics analysis, the similar of the internal
> fluctuations in may simulation systems was evaluated by comparing principal
> subspace first 10 eigenvectors) of each structural trajectory by using the
> root mean square inner product(RMSIP).
> Amadei, A., de groot, B. L., Ceruso, M. A., Paci, M., Di Nola, A. &
> Berendsen, H. J. A kinetic model for the internal motions of proteins:
> diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.
>
> Mark Abraham дµÀ£º
> xi zhao wrote:
> > Dear Gromacs users:
> > I am a new gromacs user, I want ro calculate r.m.s.i.p
> > for exploring similar in motions of two different
> > proteins, I need a script or tools to calculate it. I
> > need your help!
>
> I don't know what r.m.s.i.p is. If you want to get help, please define
> carefully what you are trying to do - even a link to a journal article
> might work. Please read carefully the gromacs manual section that
> describes what the utility programs do, in case one of them does it.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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