[gmx-users] freezing/position restraints and minimization
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
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 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
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users