Constructing a multidimensional free energy surface like a spider weaving a web. Issue 27 (18th July 2017)

• Record Type: Journal Article
• Authors: Chen, Changjun
• Is Part Of: Journal of computational chemistry. Volume 38:Issue 27(2017)
• Page Start: 2298
• Page End: 2306
• Publication Date: 2017-07-18
• Subjects: collective variable space -- free energy calculation -- constrained dynamics -- molecular dynamics; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.24881
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract : Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast‐growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow‐growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc. Abstract : This article shows that large biasing potentials cause large errors in the free energy calculation. It provides a hybrid method that performs the free energy calculation by the constraint force and performs the conformational sampling by the biasing force.