AMBER Archive (2008)

Subject: RE: AMBER: Correlation functions from iRED analysis

From: fatima.chami_at_durham.ac.uk
Date: Thu Jun 19 2008 - 08:46:22 CDT

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>
> >
> >
>
>
> --
> 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
>
> 

-- 
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
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