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/cross 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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Nov 18 2007 - 06:07:56 PST
