[gmx-users] Steepest Descent

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 1 09:07:41 CEST 2005

On Wed, 2005-08-31 at 18:58 -0400, Bob Johnson wrote:
> 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
> algorithm.
No. you can try l-bfgs instead, but the force is low enough for
proceeding to MD.
> Thanks,
> Bob Johnson
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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