[AMBER] question of analyze matrix command of ptraj

From: 张明焜 <zhangmk69.gmail.com>
Date: Mon, 9 Sep 2013 18:52:12 +0800

-- 
DEAR Professor:
       I have a question about *analyze matrix* command of ptraj,I am
trying to analyze mass-weighted covariance matrix
of  glycine(HN-CH2-CO).I prepared a mdcrd file of 200 frames,and my script
is below:
trajin prod2.mdcrd
matrix mwcovar name mwcvmat out mwcvmat.dat
analyze matrix mwcvmat out evecs.dat vecs 21
my question is why the number of eigenvalue is always equil to the number
of frames of  mdcrd,just like
if
trajin prod2.mdcrd  1 200 20
matrix mwcovar name mwcvmat out mwcvmat.dat
analyze matrix mwcvmat out evecs.dat vecs 21
the output will tell me that "Number of calculated evecs were reduced to
10" ,I support 10 is  related to the 10 frames put in.However According to
the mathematical knowledge,we can always get the total (21) nomatter how
many  frames analyzed. would you please tell me that's way?
beside,eigenvalues caculated from Ptraj and Matlab is a little
different,like below:
ptraj
matlab
error
12.93411
12.88441519
0.00385697
15.21887
15.16039194
0.003857292
20.14398
20.06658622
0.003856848
33.11686
32.98962233
0.0038569
41.22269
41.06430516
0.003856996
44.70624
44.53446793
0.003857059
48.24683
48.06145801
0.003856978
50.61372
50.41924726
0.003857113
63.66514
63.42052512
0.00385703
79.79657
79.48997437
0.003857035
93.50582
93.14655458
0.003856991
98.60892
98.23003973
0.003857071
147.6195
147.052318
0.003857008
161.49837
160.8778548
0.003857058
179.18887
178.500386
0.003857045
213.60707
212.7863417
0.003857054
249.56423
248.6053509
0.003857033
269.39794
268.3628517
0.003857048
1517.50411
1511.67354
0.00385703
1664.51352
1658.11811
0.003857029
1832.39447
1825.354023
0.003857031
---------------------------------------------------------------------
ZhangMK
+8623-63063582
Chongqing Institute of Green and Intelligent Technology of Chinese Academy
Sciences.
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Received on Mon Sep 09 2013 - 04:00:03 PDT
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