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 (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

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