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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 写道：
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
xpm2normal.csh
Description: C-Shell script
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