回复: Re: [gmx-users] r.m.s.i.p

raja raja_28 at fastmail.us
Mon Sep 18 10:26:44 CEST 2006

HI Zhao,
To compute RMSIP, you have to compute eigenvector using gromacs utility
program then from that trajectory you can compute RMSIP using a script
which I got from Tsjerk Wassenaar from this list. You can appraoch him.


On Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao"
<zhaoxiitc2002 at yahoo.com.cn> said:
> 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 <Mark.Abraham at anu.edu.au> &#20889;&#36947;&#65306;  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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  raja_28 at fastmail.us

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