Re: Restraints between ion and small molecule

From: Aron Broom (
Date: Thu Jun 26 2014 - 13:55:13 CDT

In terms of the restraint method, I'm not totally sure this makes sense.

First, there should be no need to restrain the position of the complex, so
that is fine.

But, in terms of the two conditions: The one should indeed be restrained
to the bound state as you have it (though one might ask how you determined
the distance for the bound state?, it's not clear that you would know this
in advance). But, I think the other condition should be either restrained
such that the two have a maximum distance, or, should even more
appropriately be two separate simulations of just the ammonia, and just the
gold. Because the delta-H should be the bound minus the unbound, and if
you impose no restraints within a periodic box, there may be bound
sometimes, and semi-bound others, but will never really be fully unbound.
 I could be missing something though.

Also, you might want to think about how you'll calculate that delta-H. The
pairwise interaction between the ions is easy enough (assuming, as Kenno
mentions, that you are willing to accept the MM forcefield values), but you
also need to account for all the water, which means you either need to run
the simulation for long enough that the average enthalpy of the water with
each ion stops changing, or, you need to do a Poisson-Boltzmann style of
calculation, which I suppose might also be fraught with not capturing the
quantum effects that will be important in your small charged system.


On Thu, Jun 26, 2014 at 2:21 PM, Kenno Vanommeslaeghe <> wrote:

> On 06/26/2014 02:16 PM, Kenno Vanommeslaeghe wrote:
>> then I'd have more fate in a QM approach.
> I meant "faith" of course.

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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