Jeroen van Bemmelen wrote:
Hmm, interesting...
And what about the -DFLEXIBLE definition in your mdp file during
steepest descent minimization? Do you know if that will also deform
your (SPC) water molecules? And will that deformation be corrected
again during the first equilibration step(s)?
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.
--
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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