Dear AMBER users,
I want to calculate generalized order
parameters (S2) of each
amino residues (N-H vector) by molecular
dynamics simulation and
compare it to order parameters derived from
NMR experiment.
However before that, we need to calculate the
auto time
correlation function for the vector. I performed the same
in ptraj and
find one ouput containing the information like as
follows:
Auto-correlation functions,normal type
***** Correlation functions *****
Time <P2>
0.000 1.000
1.000 0.894
2.000
0.891
3.000 0.884
4.000 0.881
5.000 0.882
6.000 0.880
7.000 0.874
8.000 0.883
9.000 0.884
10.000
0.880
.
.
.
>From the above
output we have the P2 values.
My question is that,how to calculate
S2 from the P2 values.
Can any one help in this regard ?
with regards
Biswa Ranjan Meher
Research Scholar,
IIT Guwahati, Assam-781039
Biswa Ranjan Meher
Research Scholar,
IIT
Guwahati, Assam-781039
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Received on Sun Nov 18 2007 - 06:07:56 PST
