Restraints between ion and small molecule

From: Daniel Torrente (
Date: Thu Jun 26 2014 - 11:53:49 CDT

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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