AMBER Archive (2008)Subject: Re: SV: AMBER: Correlation functions from iRED analysis
From: fatima.chami_at_durham.ac.uk
Date: Thu Jun 19 2008  11:05:36 CDT
Quoting "Samuel Genheden (a03samge)" <a03samge_at_student.his.se>:
> Hello,
>
> I have 138 residues in my protein but I have 20 prolines on which there is no
> NH vector so I'm only defining 128 vectors, although the names of the
> vectors follows the residue number so the last vector is named v138. I think
> that the names of the vectors should not matter, or?
not at all ...
did u resolve your time correlation issue?
>
> / Samuel
>
> ________________________________
>
> Från: owneramber_at_scripps.edu genom fatima.chami_at_durham.ac.uk
> Skickat: to 20080619 15:43
> Till: amber_at_scripps.edu
> Ämne: RE: AMBER: Correlation functions from iRED analysis
>
>
>
> Hi Samuel,
>
> Quoting "Samuel Genheden (a03samge)" <a03samge_at_student.his.se>:
>
> > Helo,
> >
> > I still get identical correlation functions for all the NH 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
>
> likewise, I thought there is no need to alignment of the snapshots
> it is so vague in the manual... I am having the same issue with this cal.
>
> is it 128 NH vectors or 138 cause your script shows 138 NH vectors and
> compute 128 eigenvectors ...should not they be same number!
>
>
> best wishes
> fatima
> >
> > / Samuel
> >
> >
> > Original Message
> > From: owneramber_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 NH 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
> > autocorrelation 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) 6451334
> > 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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