Determination of the solid-fluid coexistence of the n − 6 Lennard-Jones system from free energy calculations

2012 ◽  
Vol 136 (17) ◽  
pp. 174502 ◽  
Author(s):  
J. M. G. Sousa ◽  
A. L. Ferreira ◽  
M. A. Barroso
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Lennard Jones

Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On-the-Fly Approach

2020 ◽  
Author(s):  
Braden Kelly ◽  
William Smith
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
Free Energy Calculations ◽  
Partial Charge ◽  
Average Absolute Deviation ◽  
Absolute Deviation ◽  
Energy Calculations ◽  
Lennard Jones ◽  
Partial Charges ◽  
The Cost

<div>We present a methodology using fixed charge force-fields for alchemical solvation free energy calculations which accounts for the change in polarity that the solute experiences as it transfers from the gas-phase to the condensed phase. We update partial charges using QM/MM snapshots, decoupling the electric field appropriately when updating the partial charges. We also show how to account for the cost of self-polarization. We test our methodology on 30 molecules ranging from small polar to large drug-like molecules. We use Minimum Basis Iterative Stockholder (MBIS), Restrained Electrostatic Potential (RESP) and AM1-BCC partial charge methodologies. Using our method with MP2/cc-pVTZ and MBIS partial charges yields an Average Absolute Deviation (AAD) of 6.3 kJ·mol−1 in comparison with the AM1-BCC result of 8.6 kJ·mol−1. AM1-BCC is within experimental uncertainty on 10% of the data compared to 30% with our method. We conjecture that results can be further improved by using Lennard-Jones and torsional parameters refitted to MBIS and RESP partial charge methods that use high levels of theory.</div>

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

2007 ◽  
Vol 127 (21) ◽  
pp. 214108 ◽  
Author(s):  
Thomas Steinbrecher ◽  
David L. Mobley ◽  
David A. Case
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Lennard Jones

Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An OTFP Approach

2019 ◽  
Author(s):  
Braden Kelly ◽  
William Smith
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
Free Energy Calculations ◽  
Partial Charge ◽  
Experimental Uncertainty ◽  
Hydration Free Energy ◽  
Energy Calculations ◽  
Lennard Jones ◽  
Partial Charges ◽  
The Cost

We present a methodology using fixed charge force–fields for alchemical solvation free energy calculations which accounts for the change in polarity that the solute experiences as it transfers from the gas-phase to the condensed phase. We update partial charges use QM/MM snapshots, decoupling the electric field appropriately when updating the partial charges. We also show how to account for the cost of self-polarization. We test our methodology on 30 molecules ranging from small polar to large drug–like molecules.We use Minimum Basis Iterative Stockholder (MBIS), Restrained Electrostatic Potential(RESP) and AM1-BCC partial charge methodologies. Using our method with MP2/cc-pVTZ and MBIS partial charges yields an AAD that is 2.98 kJ·mol−1(0.71 kcal·mol−1) lower than AM1–BCC. AM1–BCC is within experimental uncertainty on 10% of thedata compared to 40% with our method. We conjecture that results can be further improved by using Lennard–Jones and torsional parameters refitted to MBIS and RESP partial charge methods that use high levels of theory.<br>

Alchemical Hydration Free Energy Calculations Using Molecular Dynamics with Explicit Polarization and Induced Polarity Decoupling: An On-the-Fly Approach

2020 ◽  
Author(s):  
Braden Kelly ◽  
William Smith
Keyword(s):  
Free Energy ◽  
Gas Phase ◽  
Free Energy Calculations ◽  
Partial Charge ◽  
Average Absolute Deviation ◽  
Absolute Deviation ◽  
Energy Calculations ◽  
Lennard Jones ◽  
Partial Charges ◽  
The Cost

<div>We present a methodology using fixed charge force-fields for alchemical solvation free energy calculations which accounts for the change in polarity that the solute experiences as it transfers from the gas-phase to the condensed phase. We update partial charges using QM/MM snapshots, decoupling the electric field appropriately when updating the partial charges. We also show how to account for the cost of self-polarization. We test our methodology on 30 molecules ranging from small polar to large drug-like molecules. We use Minimum Basis Iterative Stockholder (MBIS), Restrained Electrostatic Potential (RESP) and AM1-BCC partial charge methodologies. Using our method with MP2/cc-pVTZ and MBIS partial charges yields an Average Absolute Deviation (AAD) of 6.3 kJ·mol−1 in comparison with the AM1-BCC result of 8.6 kJ·mol−1. AM1-BCC is within experimental uncertainty on 10% of the data compared to 30% with our method. We conjecture that results can be further improved by using Lennard-Jones and torsional parameters refitted to MBIS and RESP partial charge methods that use high levels of theory.</div>

Free-energy calculations using classical molecular simulation: application to the determination of the melting point and chemical potential of a flexible RDX model

2016 ◽  
Vol 18 (11) ◽  
pp. 7841-7850 ◽  
Author(s):  
Michael S. Sellers ◽  
Martin Lísal ◽  
John K. Brennan
Keyword(s):  
Free Energy ◽  
Melting Point ◽  
Molecular Simulation ◽  
Chemical Potential ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Liquid Phases

Several methods are used in sequence to determine the chemical potential of atomistic RDX in the solid and liquid phases, and its corresponding melting point. Results yield the thermodynamic melting point of 488.75 K at 1.0 atm.

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