In this paper, we explore the strengths and weaknesses of a cavity-based method to calculate the excess chemical potential of a large molecular solute in a dense liquid solvent. Use of the cavity alleviates some technical problems associated with the appearance of (integrable) divergences in the integrand during alchemical particle growth. The excess chemical potential calculated using the cavity-based method should be independent of the cavity attributes. However, the performance of the method (equilibration time and the robustness) does depend on the cavity attributes. To illustrate the importance of a suitable choice of the cavity attributes, we calculate the partition coefficient of pyrene in toluene and heptane using a coarse-grained model. We find that a poor choice for the functional form of the cavity may lead to hysteresis between growth and shrinkage of the cavity. Somewhat unexpectedly, we find that, by allowing the cavity to move as a pseudo-particle within the simulation box, the decay time of fluctuations in the integrand of the thermodynamic integration can be reduced by an order of magnitude, thereby increasing the statistical accuracy of the calculation.
Skip Nav Destination
Article navigation
7 July 2018
Research Article|
July 06 2018
Addressing hysteresis and slow equilibration issues in cavity-based calculation of chemical potentials
C. R. Wand
;
C. R. Wand
1
Department of Chemistry, University of Cambridge
, Cambridgeshire CB2 1EW, United Kingdom
Search for other works by this author on:
T. S. Totton;
T. S. Totton
2
BP Exploration Operating Co. Ltd.
, Sunbury-on-Thames TW16 7LN, United Kingdom
Search for other works by this author on:
D. Frenkel
D. Frenkel
a)
1
Department of Chemistry, University of Cambridge
, Cambridgeshire CB2 1EW, United Kingdom
a)Author to whom correspondence should be addressed: [email protected]
Search for other works by this author on:
a)Author to whom correspondence should be addressed: [email protected]
J. Chem. Phys. 149, 014105 (2018)
Article history
Received:
April 19 2018
Accepted:
June 06 2018
Citation
C. R. Wand, T. S. Totton, D. Frenkel; Addressing hysteresis and slow equilibration issues in cavity-based calculation of chemical potentials. J. Chem. Phys. 7 July 2018; 149 (1): 014105. https://doi.org/10.1063/1.5036963
Download citation file:
Pay-Per-View Access
$40.00
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Citing articles via
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
CREST—A program for the exploration of low-energy molecular chemical space
Philipp Pracht, Stefan Grimme, et al.
Evaluation of the MACE force field architecture: From medicinal chemistry to materials science
Dávid Péter Kovács, Ilyes Batatia, et al.
Related Content
Calculation of the water-octanol partition coefficient of cholesterol for SPC, TIP3P, and TIP4P water
J. Chem. Phys. (December 2018)
Computational methodology for solubility prediction: Application to sparingly soluble organic/inorganic materials
J. Chem. Phys. (August 2018)
A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals
J. Chem. Phys. (November 2023)
A soft-core Gay–Berne model for the simulation of liquid crystals by Hamiltonian replica exchange
J. Chem. Phys. (November 2009)
Fast equilibration protocol for million atom systems of highly entangled linear polyethylene chains
J. Chem. Phys. (April 2016)