Dear All,
I am trying to calculate the principal moment of inertia of a molecule. I use the Ptraj to do it with the following input file:
trajin reimage.mdcrd
prnlev 6
vector vector_x :1-5 principal x out vector_x1.dat
vector vector_y :1-5 principal y out vector_y1.dat
vector vector_z :1-5 principal z out vector_z1.dat
go
I got the output files. In the output information, it shows:
JACOBI
Ixx = 992461.988 Iyy = 786996.044 Izz = 1074401.517
Ixy = -42326.388 Ixz = -5505.561 Iyz = 114921.610
ATOM 1 XXX XX 1 31.383 31.327 31.162
ATOM 2 XXX XX 1 31.540 30.351 31.012
ATOM 1 YYY YY 2 31.383 31.327 31.162
ATOM 2 YYY YY 2 31.041 31.416 30.227
ATOM 1 ZZZ ZZ 3 31.383 31.327 31.162
ATOM 2 ZZZ ZZ 3 30.457 31.129 31.482
Eigenvalues 1117740.946 995222.755 740895.848
PRINCIPAL: WARNING!!! CHECK CHIRALITY: vectors swapped!
transformVector PRINCIPAL AXIS:
ATOM 1 PP1 PP 1 31.383 31.327 31.162
ATOM 2 PP2 PP 1 30.457 31.524 31.482
PRINCIPAL, EIGENVECTORS/VALUES ARE SWAPPED: 2 0 1
And the "vector_x1.dat" output files shows:
# FORMAT: frame vx vy vz cx cy cz cx+vx cy+vy cz+vz
# FORMAT where v? is vector, c? is center of mass...
1 -0.9266 0.1976 0.3199 31.3833 31.3267 31.1625 30.4566 31.5243 31.4823
2 -0.9253 0.2027 0.3204 31.3806 31.3248 31.1550 30.4553 31.5275 31.4754
...........
Does anyone could explain the output files for me a little bit? I really don't know which value (column) I should take for the principal moment of inertia.
Thank you very much for your any help.
Esther B.
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Received on Wed Apr 04 2007 - 06:07:50 PDT
