Re: [AMBER] the better box size for calculating host-guest interaction energies

From: David A Case <>
Date: Thu, 20 Aug 2015 11:51:23 -0400

On Thu, Aug 20, 2015, Investigador Química wrote:

> You are right. For the three isolated and solvated systems generated using
> "solvateoct TIP3PBOX 11" we have:
> Box (x=y=z) triangulated 3-points waters sum of charges
> H-G 64,477 6598 -0.99950000
> H 51,248 3254 -0.16460000
> G 37,612 1321 -0.03280000
> My problem is how can I run the simulations with the water counts exactly
> matched between the bound and unbound simulations?

This is not likely to ever work in the way you want (if I understand what
you are trying to do). The fluctuations in the water-water energies,
and the box-size dependencies of the total energies, are likely to make
any direct subtraction of explicitly solvated total energies extremely
difficult to converge. This is *not* the way people in the macromolecular
or host-guest fields go about estimating association energies.

To see what is involved (and what you want to do is really quite difficult),
look at these papers:

%A J.C. Gumbart
%A B. Roux
%A C. Chipot
%T Standard Binding Free Energies from Computer Simulations: What Is the Best
%J J. Chem. Theory Comput.
%V 9
%P 794-802
%D 2012

%A J.C. Gumbart
%A B. Roux
%A C. Chipot
%T Efficient Determination of Protein-Protein Standard Binding Free Energies
from First Principles
%J J. Chem. Theory Comput.
%V 9
%P 3789-3798
%D 2013

[An aside: your values above for "sum of charges" look very odd: what is going


AMBER mailing list
Received on Thu Aug 20 2015 - 09:00:04 PDT
Custom Search