| Record |
| Author |
Bal, K.M.; Fukuhara, S.; Shibuta, Y.; Neyts, E.C. |
| Title |
Free energy barriers from biased molecular dynamics simulations |
Type |
A1 Journal article |
Year  |
2020 |
Publication |
Journal Of Chemical Physics |
Abbreviated Journal |
J Chem Phys |
| Volume |
153 |
Issue |
11 |
Pages |
114118 |
| Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
| Abstract |
Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000574665600004 |
Publication Date |
2020-09-21 |
| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
0021-9606 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
4.4 |
Times cited |
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Open Access |
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| Notes |
Japan Society for the Promotion of Science, 19H02415 18J22727 ; Fonds Wetenschappelijk Onderzoek, 12ZI420N ; This work was supported, in part, by a Grant-in-Aid for Scientific Research (B) (Grant No. 19H02415) and Grant-in-Aid for a JSPS Research Fellow (Grant No. 18J22727) from the Japan Society for the Promotion of Science (JSPS), Japan. K.M.B. was funded as a junior postdoctoral fellow of the FWO (Research Foundation – Flanders), Grant No. 12ZI420N. S.F. was supported by JSPS through the Program for Leading Graduate Schools (MERIT). The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. The authors are grateful to Pablo Piaggi for making the pair entropy CV code publicly available. |
Approved |
Most recent IF: 4.4; 2020 IF: 2.965 |
| Call Number |
PLASMANT @ plasmant @c:irua:172456 |
Serial |
6420 |
| Permanent link to this record |
