Re: [AMBER] Obtaining excess molar volumes using Molecular Dynamics

From: David Case <>
Date: Tue, 3 Dec 2019 13:51:28 +0000

On Thu, Nov 28, 2019, Raghav Arora wrote:

>I was able to run the simulations as mentioned in the simulation and
>obtain the respective curves. After this, I was wondering if there is
>some way in which we can run a simulation in which the mole fraction of
>room-temperature ionic liquids is varied and excess molar volumes of
>acetonitrile is obtained corresponding to various mole fractions.

There are a variety of ways to do this sort of calculation. The
simplest is to just remove an acetonitrile molecule, and re-run the
simulation (at constant pressure), then compare the volumes.

An overview of a variety of approaches is here:

%A J.Z. Vilseck
%A J. Tirado-Rives
%A W.L. Jorgensen
%T Determination of partial molar volumes from free energy perturbation theory
%J Phys. Chem. Chem. Phys.
%D 2015
%V 17
%P 8407-8415

Note that the method referred to in the title is not necessarily the
best way to go in all circumstances. Another good article, focussed on
proteins, but which has a good discussion of the physics involved:

%A E.A. Ploetz
%A P.E. Smith
%T Infinitely Dilute Partial Molar Properties of Proteins from Computer Simulation
%J J. Phys. Chem. B
%V 118
%P 12844-12854
%D 2014

...hope this helps....dac

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Received on Tue Dec 03 2019 - 06:00:04 PST
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