Next Article in Journal
LES and Wind Tunnel Test of Flow around Two Tall Buildings in Staggered Arrangement
Next Article in Special Issue
An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction
Previous Article in Journal
Recent Progress in First-Principles Methods for Computing the Electronic Structure of Correlated Materials
Previous Article in Special Issue
Ionic Liquids Treated within the Grand Canonical Adaptive Resolution Molecular Dynamics Technique
Article

Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers

1
Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
2
Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), UNC-CONICET, Córdoba X5000HUA, Argentina
3
Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
*
Author to whom correspondence should be addressed.
Computation 2018, 6(2), 27; https://doi.org/10.3390/computation6020027
Received: 24 January 2018 / Revised: 26 February 2018 / Accepted: 19 March 2018 / Published: 21 March 2018
(This article belongs to the Special Issue Computation in Molecular Modeling)
In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD), adaptive-biasing forces (ABF), and on-the-fly parameterization (OTFP). We construct a simple two-dimensional potential-energy surfaces (PES) that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables. View Full-Text
Keywords: molecular dynamics; metadynamics; adaptive-biasing force algorithm; temperature-acceleration; on-the-fly parameterization molecular dynamics; metadynamics; adaptive-biasing force algorithm; temperature-acceleration; on-the-fly parameterization
Show Figures

Figure 1

MDPI and ACS Style

Paz, S.A.; Abrams, C.F. Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers. Computation 2018, 6, 27. https://doi.org/10.3390/computation6020027

AMA Style

Paz SA, Abrams CF. Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers. Computation. 2018; 6(2):27. https://doi.org/10.3390/computation6020027

Chicago/Turabian Style

Paz, S. A., and Cameron F. Abrams. 2018. "Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers" Computation 6, no. 2: 27. https://doi.org/10.3390/computation6020027

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop