Computational solvation dynamics: Implementation, application, and validation

Schröder, Christian; Heid, Esther

doi:10.1016/bs.arcc.2020.07.001

Cited by 3 publications

(5 citation statements)

References 164 publications

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“…To investigate the detailed dynamics of solvent reorientation upon changing the description of the solute from the MM to the SQM level of theory, we resort to ideas from computational spectroscopy, specifically the computation of the normalized Stokes shift

from non-equilibrium MD simulations.

is defined as [ 57 , 58 ]:

where

is the time-dependent frequency of the emitted fluorescence light of the probe molecule’s chromophore. In computation, one assumes that changes in interactions between the solute and the solvent leading to

are purely electrostatic in nature.…”

Section: Methodsmentioning

confidence: 99%

“…In both cases, the solvent water has to reorient itself following a change in the charge distribution of the solute. Therefore, we adopted the computational approach to compute

[ 57 , 58 ] as follows. We used starting configurations equilibrated either at (i) the MM level of theory or (ii) the MULL(solv) intermediate state, and restarted simulations with the full SQM/MM description of interactions.…”

Section: Methodsmentioning

confidence: 99%

Section: Dynamics Of Solvent Reorientationmentioning

confidence: 99%

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Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes

2023

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Non-equilibrium work switching simulations and Jarzynski’s equation are a reliable method for computing free energy differences, ΔAlow→high, between two levels of theory, such as a pure molecular mechanical (MM) and a quantum mechanical/molecular mechanical (QM/MM) description of a system of interest. Despite the inherent parallelism, the computational cost of this approach can quickly become very high. This is particularly true for systems where the core region, the part of the system to be described at different levels of theory, is embedded in an environment such as explicit solvent water. We find that even for relatively simple solute–water systems, switching lengths of at least 5 ps are necessary to compute ΔAlow→high reliably. In this study, we investigate two approaches towards an affordable protocol, with an emphasis on keeping the switching length well below 5 ps. Inserting a hybrid charge intermediate state with modified partial charges, which resembles the charge distribution of the desired high level, makes it possible to obtain reliable calculations with 2 ps switches. Attempts using step-wise linear switching paths, on the other hand, did not lead to improvement, i.e., a faster convergence for all systems. To understand these findings, we analyzed the solutes’ properties as a function of the partial charges used and the number of water molecules in direct contact with the solute, and studied the time needed for water molecules to reorient themselves upon a change in the solute’s charge distribution.

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from non-equilibrium MD simulations.

is defined as [ 57 , 58 ]:

where

are purely electrostatic in nature.…”

Section: Methodsmentioning

confidence: 99%

“…In both cases, the solvent water has to reorient itself following a change in the charge distribution of the solute. Therefore, we adopted the computational approach to compute

Section: Methodsmentioning

confidence: 99%

Section: Dynamics Of Solvent Reorientationmentioning

confidence: 99%

See 1 more Smart Citation

Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes

2023

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show abstract

Section: Dynamics Of Solvent Reorientationmentioning

confidence: 99%

“…In both cases, solvent water has to reorient itself following a change in charge distribution of the solute. We, therefore, adopted the computational approach to compute S(t) [56,57] as follows. We used starting configurations equilibrated either at (i) the MM level of theory or (ii) the MULL(solv) intermediate state, and restarted simulations with the full SQM/MM description of interactions.…”

Section: Dynamics Of Solvent Reorientationmentioning

confidence: 99%

Exploring Routes to Enhance the Calculation of Free Energy Differences via Nonequilibrium Work SQM/MM Switching Simulations by Using Hybrid Charge Intermediates Between MM and SQM Level of Theory or Non-linear Switching Schemes

Schöller¹,

Woodcock²,

Boresch³

2023

Preprint

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Nonequilibrium work switching simulations and Jarzynski’s equation are a reliable method to compute free energy differences, ΔAlow→high, between two levels of theory, such as a pure molecular mechanical (MM) and a quantum mechanical/molecular mechanical (QM/MM) description of a system of interest. Despite the inherent parallelism, the computational cost of this approach can quickly get very high. This is particularly true for systems where the core region, the part of the system to be described at different levels of theory, is embedded in an environment, such as explicit solvent water. We find that even for relatively simple solute–water systems, switching lengths of at least 5 ps are necessary to compute ΔAlow→high reliably. In this study, we investigate two approaches towards an affordable protocol, with emphasis on keeping the switching length well below 5 ps. Inserting a hybrid charge intermediate state with modified partial charges which resembles the charge distribution of the desired high level makes it possible to obtain reliable calculations with 2 ps switches. Attempts using step-wise linear switching paths, on the other hand, did not lead to improvement, i.e., faster convergence for all systems. To understand these findings, we analyzed the solutes’ properties as a function of partial charges used, the number of waters in direct contact with the solute, and studied the time needed for water molecules to reorient themselves upon a change in the solute’s charge distribution.

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Interrogating the mechanism of the solvation dynamics in BmimBF4/PC mixtures: A cooperative study employing time-resolved fluorescence and molecular dynamics

Smortsova

Miannay

Gustavsson

et al. 2021

Journal of Molecular Liquids

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Computational solvation dynamics: Implementation, application, and validation

Cited by 3 publications

References 164 publications

Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes

Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes

Exploring Routes to Enhance the Calculation of Free Energy Differences via Nonequilibrium Work SQM/MM Switching Simulations by Using Hybrid Charge Intermediates Between MM and SQM Level of Theory or Non-linear Switching Schemes

Interrogating the mechanism of the solvation dynamics in BmimBF4/PC mixtures: A cooperative study employing time-resolved fluorescence and molecular dynamics

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