AMBER Archive (2009)

Subject: [AMBER] To find radial distribution curve

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Thu Mar 26 2009 - 12:16:07 CDT

Dear all,
             The tutorials given with amber are simulation for proteins and
nucleic acids. I wanted to do a simulation of a box of water. So the
procedure I adopted is as follows

    First I took an empty file and considered it to be my molecule (through
loadpdb). Then I solvated it with TIP3PBOX water. Now I have done simulation
of this solvated molecule.
1. My first question is that is the procedure which I have adopted is right?
2. How do I get radial distribution function of the simulated water system?
3. How do I interpret sander output file of trajectories? This file consists
of several columns, so where can I know which column dictates what.

Kindly help me with this above queries.Thanx in advance. 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber