TY - JOUR

T1 - Overcoming orthogonal barriers in alchemical free energy calculations

T2 - on the relative merits of λ-variations, λ-extrapolations, and biasing

AU - Hahn, David F.

AU - König, Gerhard

AU - Hünenberger, Philippe H.

N1 - Authored in non-UK institution

PY - 2020/3/10

Y1 - 2020/3/10

N2 - Alchemical free energy calculations using conventional molecular dynamics and thermodynamic integration rely on simulations performed at fixed values of the coupling parameter λ. When multiple conformers in equilibrium are separated by high barriers in the space orthogonal to λ, proper convergence may require extremely long simulations. Four main strategies can be employed to address this orthogonal-sampling problem: (a) λ-variations, where λ can change along the simulations to circumvent barriers; (b) λ-extrapolations, where statistical information is transferred between λ-points; (c) specific biasing, where orthogonal barriers are reduced using a biasing potential designed specifically for the system; and (d) generic biasing, where orthogonal barriers are reduced using a generic approach. Here, we investigate the relative merits of the first three strategies considering two benchmark systems. The KXK system involves a mutation of the central residue in a tripeptide to a glycine and the XTP system involves a hydrogen-to-bromine mutation in the base of a nucleotide. Three sampling methods are compared, the latter two involving λ-variations: molecular dynamics simulations with fixed λ-points, Hamiltonian replica exchange, and the recently introduced conveyor belt method. Two free energy estimators are applied, the second one involving λ-extrapolations: thermodynamic integration with Simpson quadrature and the multistate Bennett acceptance ratio. Finally, three different seeding schemes are considered for the generation of the initial configurations. For both benchmark systems, λ-extrapolations are found to provide little gain, whereas λ-variations can significantly enhance the convergence. They are sufficient on their own if the orthogonal barriers are low in at least one state (e.g., the glycine state in KXK). However, if the orthogonal barriers are high over the entire λ-range (e.g., the XTP system), λ-variations are only effective when applied together with a specific biasing for introducing such a low-barrier state.

AB - Alchemical free energy calculations using conventional molecular dynamics and thermodynamic integration rely on simulations performed at fixed values of the coupling parameter λ. When multiple conformers in equilibrium are separated by high barriers in the space orthogonal to λ, proper convergence may require extremely long simulations. Four main strategies can be employed to address this orthogonal-sampling problem: (a) λ-variations, where λ can change along the simulations to circumvent barriers; (b) λ-extrapolations, where statistical information is transferred between λ-points; (c) specific biasing, where orthogonal barriers are reduced using a biasing potential designed specifically for the system; and (d) generic biasing, where orthogonal barriers are reduced using a generic approach. Here, we investigate the relative merits of the first three strategies considering two benchmark systems. The KXK system involves a mutation of the central residue in a tripeptide to a glycine and the XTP system involves a hydrogen-to-bromine mutation in the base of a nucleotide. Three sampling methods are compared, the latter two involving λ-variations: molecular dynamics simulations with fixed λ-points, Hamiltonian replica exchange, and the recently introduced conveyor belt method. Two free energy estimators are applied, the second one involving λ-extrapolations: thermodynamic integration with Simpson quadrature and the multistate Bennett acceptance ratio. Finally, three different seeding schemes are considered for the generation of the initial configurations. For both benchmark systems, λ-extrapolations are found to provide little gain, whereas λ-variations can significantly enhance the convergence. They are sufficient on their own if the orthogonal barriers are low in at least one state (e.g., the glycine state in KXK). However, if the orthogonal barriers are high over the entire λ-range (e.g., the XTP system), λ-variations are only effective when applied together with a specific biasing for introducing such a low-barrier state.

UR - http://www.scopus.com/inward/record.url?scp=85081884898&partnerID=8YFLogxK

UR - https://www.research-collection.ethz.ch/handle/20.500.11850/406658

U2 - 10.1021/acs.jctc.9b00853

DO - 10.1021/acs.jctc.9b00853

M3 - Article

C2 - 31995374

AN - SCOPUS:85081884898

SN - 1549-9618

VL - 16

SP - 1630

EP - 1645

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

IS - 3

ER -