[AMBER] To find radial distribution curve

From: nicholus bhattacharjee <nicholusbhattacharjee.gmail.com>
Date: Thu, 26 Mar 2009 17:16:07 +0000

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)
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Received on Fri Mar 27 2009 - 01:16:11 PDT
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