isotropic scaling of coordinates during MD

From: Giulio Rastelli <>
Date: Sat 14 Apr 2001 13:35:48 +0200

Dear all,

I am performing a MD simulation of a protein in a periodic box of
water using Ewald
I used isotropic position scaling (ntp=1) on a atom-basis (npscal=0).
Since the box made with leap is much larger than what needed to reach
the target density of 1, the box correctly shrinks during MD.
As a result, coordinates of the protein shrink to unphysical bond
lenghts and angles.
Subsequent minimization of the coordinates resulting from MD restores
to correct bond lenghts and angles, but it seems to me that, since
the box shrinks so much ( more than 8 angstrom), and the coordinates
shrink of about 0.5 angstroms, the minimization would
start from a very unfavorable set of coordinates!.

I would like to hear your feedback

Happy Easter...

Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
tel 0039-059-2055145
fax 0039-059-2055131
Received on Sat Apr 14 2001 - 04:35:48 PDT
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