a few more questions

From: Jake Isaacs <rjisaa0_at_pop.uky.edu>
Date: Mon 12 Feb 2001 13:37:16 -0500

When doing a series of constant pressure minimizations and MD simulations,
should I always have ntx=7, since the periodic box (or truncated octohedron)
dimensions will change? It seems that having an updated system smaller than
that in the prmtop file would create vacuum at the edges, hampering
equillibration. Or conversely, having an updated system larger than that in
the prmtop file would result in solvent molecules outside the "box", the
effects of which I couldn't even predict. Will ntx=7 work when going from
minimization to MD, since there are no velocities in minimization? There
doesn't seem to be an option for only reading in coordinates and box
dimensions. If I wanted to rescale velocities between two MD runs, while
preserving "box" dimensions, how would I tell sander to ignore the "old"
velocities? Actually, is there merit to rescaling velocities as part of
equillibration in order to dampen out oscillations caused by initially "bad"
solvent and internal solute positions? Along a similar line, is there a
point at which I should shift to constant volume (i.e. a point at which
constant pressure should not be used)?

That should be enough for today. Thanks again.

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Received on Mon Feb 12 2001 - 10:37:16 PST
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