AMBER Archive (2007)

Subject: AMBER: How to calculate S2 from P2 using ptraj ?

From: brmeher_at_iitg.ernet.in
Date: Sat Nov 17 2007 - 00:40:31 CST

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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