Re: [AMBER] solvent and counter ions

From: Taufik Al-Sarraj <>
Date: Thu, 05 Mar 2009 18:16:24 -0500

Thank you Thomas for clarifying this. Is it acceptable to add counter
ions first and then water (solvent)? and then allow the solvent-ions to
relax in an initial minimization where the solute is fixed? (avoiding
the process of selecting and deleting water molecules)

In "Molecular Dynamics Simulations of the 136 Unique Tetranucleotide
Sequences of DNA Oligonucleotides..." Biophysical Journal Vol.89
(3721-3740) 2005. I couldn't find the reason for choosing K+ over Na+ as
a counterion. Is there one? Or is it a preference?


Thomas Cheatham III wrote:
>> 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.
> --tec3
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Received on Fri Mar 06 2009 - 01:25:45 PST
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