AMBER Archive (2009)

Subject: Re: [AMBER] solvent and counter ions

From: Thomas Cheatham III (
Date: Wed Mar 04 2009 - 15:49:35 CST

> In literature, after water (solvent) is added few water (solvent)
> molecules are removed and replaced by counter ions, what is the reason
> behind this? is it incorrect to add solvent and counter ions without
> removing any solvent atoms?

The density of water leads to a fairly dense system with very little space
between water molecules; it is very unlikely that you will have
spontaneous holes big enough for an ion. As many common ions are similar
in size to a water (sort of), swapping with a water (and deleting) the
water makes sense. The algorithm will place an ion if the waters are not
too close.

All of this points out that the initial water and ion distribution will
not be optimal/realistic and that careful massaging will be necessary to
relax the water and ions (usually with the solute restrained). There are
many protocols for this. In cases where the overlap between ions and
water is extreme, initially you may have to do minimization with the
charges turned off (which can be performed through the nmropt=1 options
and weight changes on ELEC).

Sometimes the algorithms break down and atoms overlap; this is often
evidenced by extremely large electrostatic energies. The "checkoverlap"
command in ptraj can look for overlapping atoms.


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