[gmx-users] freezing/position restraints and minimization

David Mobley dmobley at gmail.com
Mon Mar 19 16:15:29 CET 2007


> > I ask this, because I read on severel places (e.g. the online mdp
> > options manual and in one of the tutorials) that you could use the -
> > DFLEXIBLE definition to "allow steepest descent to minimize further".
> > So I've used it for most of my minimizations up til now, assuming
> > that was the right thing to do.

> it is fine, but your bond lengths and bond angle in water will be
> slightly off the equilibrium values. This will be corrected during th
> eequilibration.

Just to be ornery, I'd like to point out that the idea of
"minimization" is that you end up at a potential energy minimum for
the same Hamiltonian with which you'll be simulating. If your water
deforms during minimization but is rigid during simulation, this is
not what's going on: You're "minimizing" to a minimum that belongs to
a different Hamiltonian than the one in which you're simulating.

I guess that's just to say I'd like to see the other minimizers aside
from "steep" be compabible with constraints (i.e. rigid water).


> --
> David.
> ________________________________________________________________________
> 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://folding.bmc.uu.se
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