[gmx-users] Steepest Descent

Bob Johnson robertjo at physics.upenn.edu
Thu Sep 1 00:58:30 CEST 2005

Hello everyone,
My system consists of an infinite nanotube and single stranded DNA. I'm trying
to perform energy minimization to study the minimum energy conformation of the
DNA on the nanotube. I'm using steepest descent but can't get it to work. I get
the following message:

Steepest Descents converged to machine precision in 2381 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -2.5976504e+04
Maximum force     =  1.4356376e+01 on atom 1914
Norm of force     =  1.3578325e+02

When I look at the trajectory calculated during the energy minimization, there
is no perceptible change in the DNA conformation on the nanotube. I've tried
adjusting the step size and also ran md before steep to make sure that the DNA
was close enough to feel the presence of the nanotube but nothing seems to
work. Is there a way to get better sampling out of the steepest descent
Bob Johnson

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