AMBER Archive (2002)

Subject: Potential Energy and RMS-Deviation Issues

From: mdk7p_at_cms.mail.virginia.edu
Date: Thu Aug 01 2002 - 10:01:07 CDT

Hello everyone,

I am analyzing a few recent MD runs, and I've come across a few
strange results that I wanted to get some advice on from the pros.

I ran a 1ns production over the course of 5 200ps runs on a triplex
(no water, PME used, Zn2+ counterions, 1fs timestep, 300K, 5kcal DNA
and 25 kcal ion restraints throughout the run). When I plotted the
potential energy over the course of the calculation, it stayed steady
throughout each individual run, and dropped ~100 kcal/mol between
each restart. As a result, my graph looks like a set of stairs. Is
this common, or did I foul up somewhere?

Also, I ran a 1ns production over 5 200ps runs on a duplex in a
waterbox (5500 waters, PME used, Zn2+ counterions, 2fs timestep,
300K, no restraints). The PE was fine in this case, but the RMS-
deviation seemed to start at 0 and drift gradually up to 1-1.5A after
each restart. Is this supposed to happen?

Thanks!!

Best,

Mike Keller
UVA Chemistry Dept.