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.C11 ired :4.O2
vector v2 :5.C11 ired :5.O2
matrix ired name residue_anal
analyze matrix residue_anal vecs 6 out ired.vec thermo
vector v1 :4.C11 corrired :4.O2 order 2 modes ired.vec beg 1 end 6 npair 1
vector v2 :5.C11 corrired :5.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
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Received on Sun Jun 22 2008 - 06:07:15 PDT
