AMBER Archive (2001)

Subject: ptraj correlation command

From: Troy Bothwell (tbothwe1_at_bigred.unl.edu)
Date: Sat Apr 21 2001 - 09:23:40 CDT

Hello all,

I was using the ptraj correlation command to gain insight into to movement
of a dye attached to DNA. However, the amber manual does not clearly
describe the output file that is generated. I'm not sure what some of the
information is telling me specifically:

1. What is Rrigid and Rave?
2. How does the 1/r^3 and 1/r^6 fit into this calculation
3. C(t) and P2(t) have nearly identical values. I believe that P2(t) is the
2nd legendre polynomial. Could you describe their implementation.
4. What is R(t) telling me?

The output is attached for your review. There may be a resource that I can
go to, which will tell me everything I need to know.

Thanks for your time,

Troy Bothwell

Attachment Converted: "c:\eudora\attach\Correlation.out"