Re: [AMBER] MD_Box_size_and_counterions_counting_general_rule

From: David A Case <>
Date: Thu, 25 Oct 2018 10:18:59 -0400

On Thu, Oct 25, 2018, Antonio Amber Carlesso wrote:
> Is there any general rule to follow regarding the size of the box compared
> to the molecular object(s) investigated?

Commonly, Amber users include enough solvent around a molecular that
that there is at least 12-15 Å between any solute atom and the edge of
the box. This is typically done using the solvateBox or solvateOct
commands in tleap.

This is a compromise between accuracy and speed. It can be worth
experimenting with large box sizes to see what happens.

> In addition, counterions that should be added to reflect “physiologic
> condition”..
> Is there any general rule when it is reasonable to substract the volume of
> the solute from the overall volume and when the volume of the solute can be
> neglected in the overall counterions calculations?

There is no general rule here. Use of "physiologic conditions" might
make sense if you are expecting to compare with studies in cells; for
comparisons to in vitro work, of course, different salt conditions might
be more appropriate.

I generally like to prepare simulations such that the *molal*
concentration of salt is the same as that reported for whatever
experiment seems most relevant. This avoids all questions of the solute
partial molar volume. But if the differences are important to you, you
would really need to use multiple box sizes, and look at the effective
concentrations of ions far from the solute in your simulation. This is
occasionally done with highly charged solutes like nucleic acids, or in
studies where the distribution of ions is being investigated. It is
rarely done if properties of the solute are of greatest importance.


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Received on Thu Oct 25 2018 - 07:30:03 PDT
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