AMBER Archive (2003)

Subject: Water density and force output questions

From: dianah_at_unm.edu
Date: Fri Mar 07 2003 - 17:36:41 CST

Two questions:
1. We find that the TIPS3P water in our water cap (35A, surrounding a
key region of our protein) always spontaneously contracts to a radius
smaller than it started with, and equilibrates at a density about 10%
too high, even though it starts at a density below 1. Is this normal,
or are we doing something wrong? If it is normal, does it affect
rates of diffusion in this solvent? Other properties? If so, are
other water models better?

2. Is there a way to have FORCES, rather than energies, output,
either during an MD run or from trajectory files after the run? We've
looked through all the standard AMBER software, including the source
code, and find that forces are (of course) computed during the MD
runs, and that there are many ways to output and analyze energies, but
are frustrated to find no standard way to write out forces. Do we
need to modify the program (this does not seem trivial), or is there
something obvious and standard that we've missed?

David Keller