AMBER Archive (2008)

Subject: Re: AMBER: Correlation functions from iRED analysis

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Jun 19 2008 - 11:06:36 CDT

Have you ever read the original paper of "model-free approach" by Lipari and
Szabo?
JACS (1982) 104:4546-4559
Szabo was mentor of my boss.

Have you ever read the original paper of "iRED" by Prompers and Brushweiler?
JACS (2002)124:4522-4534
Brushweiler is in the same institute of mine.

We published a paper, JMB (2007) 374: 977-992.

Accoriding to Szabo's "model-free" paper, the order parameter is related to
the internal motion
not the overall motion.
By superimposing your trajectory you can remove the overall motion.
Then get auto correlation function using 128 vectors and angles b/w itselves
along the time and using Legendre polinomial
2nd order. (see the papers for detail)

If you want to calculate only order parameters, you don't need matrix at
all.

On Thu, Jun 19, 2008 at 9:46 AM, <fatima.chami_at_durham.ac.uk> wrote:

> Quoting "Samuel Genheden (a03samge)" <a03samge_at_student.his.se>:
>
> > Hello, agaim
> >
> > Sorry to ask so many questions, but this is kind of new for me. Why is it
> a
> > bad thing that iRED uses cross correlation functions? Is it harder to
> > calculate order parameters from these?
>
>
> Hi, this is not what the manual says
> I think you can do bot cross and auto according to the manual
>
> we need to get more support on this matter and let the expert feed us back
>
> best wishes
> Fatima
> >
> > / Samuel
> >
> >
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu on behalf of Myunggi Yi
> > Sent: Thu 6/19/2008 3:14 PM
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Correlation functions from iRED analysis
> >
> > Don't use ired.
> > iRED uses cross correlation functions.
> >
> > On Thu, Jun 19, 2008 at 9:10 AM, Samuel Genheden (a03samge) <
> > a03samge_at_student.his.se> wrote:
> >
> > > Helo,
> > >
> > > I still get identical correlation functions for all the N-H vectors,
> even
> > > though I do a RMS fit. And I thought one of the advantages of doing an
> > iRED
> > > analysis was that I should not do an RMS fit. Isn't that correct?
> > >
> > > / Samuel
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: owner-amber_at_scripps.edu on behalf of Myunggi Yi
> > > Sent: Thu 6/19/2008 2:52 PM
> > > To: amber_at_scripps.edu
> > > Subject: Re: AMBER: Correlation functions from iRED analysis
> > >
> > > On Thu, Jun 19, 2008 at 6:22 AM, Samuel Genheden (a03samge) <
> > > a03samge_at_student.his.se> wrote:
> > >
> > > >
> > > > Hello, Amber users
> > > >
> > > > I'm studying a protein using MD and would like to calculate
> correlation
> > > > functions with the iRED method in order to compare order parameters
> from
> > > > NMR. My protein is 138 residues long and contains 10 prolines, and
> > > therefore
> > > > I have 128 N-H vectors. I'm using Amber10. My input file looks like
> > this:
> > > >
> > > > trajin ../mdcrd5.gz
> > > > trajin ../mdcrd6.gz
> > > > vector v2 :2_at_N ired :2_at_H
> > > > vector v3 :3_at_N ired :3_at_H
> > > > ..
> > > > vector v138 :138_at_N ired :138_at_H
> > > > matrix ired name matired order 2
> > > > analyze matrix matired vecs 128 out ired.vec
> > > > vector v2 :2_at_N corrired :2_at_H order 2 modes ired.vec beg 1 end 128
> npair
> > > 1
> > > > vector v3 :3_at_N corrired :3_at_H order 2 modes ired.vec beg 1 end 128
> npair
> > > 2
> > > > ..
> > > > vector v138 :138_at_N corrired :138_at_H order 2 modes ired.vec beg 1 end
> 128
> > > > npair 128
> > > > analyze timecorr vec1 v2 tstep 10.0 tcorr 10000 out Ired/v2.out
> > > > analyze timecorr vec1 v3 tstep 10.0 tcorr 10000 out Ired/v3.out
> > > > ..
> > > > analyze timecorr vec1 v138 tstep 10.0 tcorr 10000 out Ired/v138.out
> > > >
> > > > (I've have also tried to break it up in two ptraj scripts, since the
> > > manual
> > > > is a little bit vague if this is neccessary.) The problem is that all
> > the
> > > > correlation functions calculated, v2.out, v3.out, .. v138.out is the
> > > same,
> > > > i.e. all the output files contains the same numbers. What am I doing
> > > wrong?
> > > > I can hardly believe that all the correlation functions should be
> > > identical.
> > > >
> > > > And when I'm at writing - what is the best way to obtain the order
> > > > parameters from the correlation functions?
> > > >
> > >
> > > To get the generalized order parameters, you need to calculate
> > > auto-correlation functions after "rms fitting".
> > > Then fit your graph with single or double exponential functions.
> > > The plateau corresponds to the S^2.
> > >
> > > >
> > > > Best regards, Samuel
> > > >
> > >
> > >
> > >
> > > --
> > > Best wishes,
> > >
> > > Myunggi Yi PhD
> > > ==================================
> > > KLB 419
> > > Institute of Molecular Biophysics
> > > Florida State University
> > > Tallahassee, FL 32306
> > >
> > > Office: (850) 645-1334
> > > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> <
> http://www.scs.fsu.edu/%7Emyunggi>
> > >
> > >
> >
> >
> > --
> > Best wishes,
> >
> > Myunggi Yi PhD
> > ==================================
> > KLB 419
> > Institute of Molecular Biophysics
> > Florida State University
> > Tallahassee, FL 32306
> >
> > Office: (850) 645-1334
> > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi>
> >
> >
>
>
> --
> Dr. F.Chami
> Science Lab.
> Department of Chemistry
> Durham University
> South Road Durham, DH 1 4 LE
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
Best wishes,

Myunggi Yi PhD
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu