AMBER Archive (2007)Subject: AMBER: How to calculate S2 from P2 using ptraj ?
From: brmeher_at_iitg.ernet.in
Date: Sat Nov 17 2007  00:34:11 CST
Dear AMBER users,
I want to calculate
generalized order parameters (S2) of each
amino residues (NH
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:
Autocorrelation 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, Assam781039

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