AMBER Archive (2006)

Subject: Re: AMBER: positional restraints & constant pressure

From: David A. Case (
Date: Fri Feb 03 2006 - 10:40:53 CST

On Thu, Feb 02, 2006, Kateryna Miroshnychenko wrote:
> I would like to clarify some questions concerning the usage of positional
> restrains(ntr=1) with constant pressure(ntb=2, ntp=1).
> According to the Amber Manual ntp=1 means isotropic position scaling.
> Does this mean that the coordinates of the center of mass of my
> molecule will be shifted as a result of pressure scaling?


> If so, than how the coordinates of my molecule can be restrained to
> the coordinates of the reference structure? Are the centres of masses
> of these two molecules superimposed before restraints are applied?

The center of mass of the reference molecule is scaled in the same way as the
"real" molecule when pressure scaling is invoked. There is no particular
constraint that forces the centers of mass of the real and reference system to
be the same. But if all the atoms of the real structure are close to all of
the atoms of the reference structure, then their centers of mass will be close
as well.

> As far as I've understood while reading the answers from the AMBER
> mail archive, the usage of ntr=1 with small force constant, less than
> 5kcal/(molA2), and ntb=2, ntp=1 should not give any problems. Is it
> just due to the small value of force constant? Can the usage of ntb=2
> with ntr=1 during all the md simulation cause some potential problems?

This should not cause problems. Of course, positional restraints are
artificial forces, and there is inevitably some lack of realism involved in
using them.

...good luck...dac

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