AMBER Archive (2005)

Subject: AMBER: Analysing my simulation data..

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Sat Jun 18 2005 - 03:32:13 CDT

Dear Amber users,

I am a novel user of Amber and I have done my
simulation on micelle strucure in explicit water.

Here I would like to get some advice and guidance from
all the professionals out there the procedure that I
must follow to get a reliable results of my analysis.

I would like to calculate properties like
RMSD value,
Radius of Gyration, and
H-bond for my micelle structure.

In order to calulate the above properties do I need to
reimage the micelle structure?

Is there any other pre-adjustments or pre-setup I need
to do with the output files such as xxxx.mdcrd,
xxxx.out, xxxx.rst before starting calculation?

I really appreciate your kind advice and guidance.

Thank you
Vijay.

                
___________________________________________________________
How much free photo storage do you get? Store your holiday
snaps for FREE with Yahoo! Photos http://uk.photos.yahoo.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu