AMBER Archive (2008)

Subject: AMBER: cross correlation function using iRED matrix

From: fatima.chami_at_durham.ac.uk
Date: Wed Jun 18 2008 - 12:07:25 CDT

Hi folks,

I am trying to calculate the cross correlation time function according to the
ired approach. The ired eigen vector file shows undefined values:

 Eigenvector file: IRED
    2 2
    1.00000 1.00000
 ****
    1 1.10699
   -0.70711 0.70711
 ****
    2 0.89301
   -0.70711 -0.70711

my ptraj script is as follow:
-------------------------------------------------------
trajin stack8w_md8_no_wat.mdcrd
rms first
vector v1 :4_at_C11 ired :4_at_O2
vector v2 :5_at_C11 ired :5_at_O2
matrix ired name residue_anal
analyze matrix residue_anal vecs 6 out ired.vec thermo
vector v1 :4_at_C11 corrired :4_at_O2 order 2 modes ired.vec beg 1 end 6 npair 1
vector v2 :5_at_C11 corrired :5_at_O2 order 2 modes ired.vec beg 1 end 6 npair 2
analyze timecorr vec1 v1 vec2 v2 out vired.out
----------------------------------------------------------
 
The logfile of ptraj

 Checking coordinates: stack8w_md8_no_wat.mdcrd
ptraj(), analyzeMatrix: parameter "thermo" only
works for MATRIX_MWCOVAR, returning.
FYI: Number of read evecs is 2, number of requested evecs is 6
WARNING in ptraj(), analyze timecorr: only calculating IRED corr for vec1,
ignoring vec2

best wishes
Fatima
-----------------------------------------------------------------------
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