David,
> 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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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