Re: Restraints between ion and small molecule

From: Kenno Vanommeslaeghe (
Date: Thu Jun 26 2014 - 13:16:31 CDT

The approach is fundamentally correct, but may take a long time to
converge. The end result will be a direct reflection of the potential
you're using, so if the latter is not carefully and thoroughly optimized
(which is quite difficult to do for your particular system), the result is
likely to be meaningless. Assuming an enthalphy (delta-H) is really what
you're after, then I'd have more fate in a QM approach. If MM is the
metaphorical hammer, I don't think the problem you're trying to solve can
be represented by a nail.
On 06/26/2014 12:53 PM, Daniel Torrente wrote:
> Dear All,
> I am running a NPT simulation of a metal ion (Au+1) and a small molecule
> (ammonia). I am trying to calculate the delta H between a bounded
> (ion+ammonia) and unbounded (ion) condition. Right now, I am running the
> bonded condition with just a restraint in the distance between the ion and
> the small molecule using COLVAR distance, this maintenance the distance of
> the two atoms but the complex move inside the box. On the other hand, in
> the unbonded condition i'm not using any restrain for the ion so is moving
> also freely inside the box.
> Is this approach correct? if not should I restrain the movement of the
> ion-ammonia complex in the bonded condition, as well as, restrain the ion
> movement in the unbonded condition? Or is there a better combination of
> restraints for this type of delta H calculation with small complexes?
> Thanks in advance
> Daniel Torrente
> University of Texas at San Antonio

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