scholarly journals Polarizable Simulations with Second-Order Interaction Model—Force Field and Software for Fast Polarizable Calculations: Parameters for Small Model Systems and Free Energy Calculations

2009 ◽  
Vol 5 (11) ◽  
pp. 2935-2943 ◽  
Author(s):  
George A. Kaminski ◽  
Sergei Y. Ponomarev ◽  
Aibing B. Liu
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Interaction Model ◽  
Second Order ◽  
Free Energy Calculations ◽  
Model Systems ◽  
Energy Calculations ◽  
Order Interaction ◽  
Small Model

scholarly journals Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side-chain analogues

2013 ◽  
Vol 34 (14) ◽  
pp. 1241-1250 ◽  
Author(s):  
Xinbi Li ◽  
Sergei Y. Ponomarev ◽  
Qina Sa ◽  
Daniel L. Sigalovsky ◽  
George A. Kaminski
Keyword(s):  
Force Field ◽  
Interaction Model ◽  
Second Order ◽  
Side Chain ◽  
Order Interaction

scholarly journals Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

2021 ◽  
Author(s):  
Lauren Nelson ◽  
Sofia Bariami ◽  
Chris Ringrose ◽  
Joshua Horton ◽  
Vadiraj Kurdekar ◽  
...  
Keyword(s):  
Free Energy ◽  
Force Field ◽  
High Throughput ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Simulation Package ◽  
Alchemical Free Energy Calculations

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field approach has been developed to facilitate the automated derivation of potential energy function parameters for modelling protein-ligand binding. To date the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free energy calculation molecular dynamics simulation package SOMD. The implementation is validated by demonstrating the reproducibility of absolute hydration free energies computed with the QUBE force field across the SOMD and GROMACS software packages. We further demonstrate, by way of a case study involving two series of non-nucleoside inhibitors of HIV-1 reverse transcriptase, that the availability of QUBE in a modern simulation package that makes efficient use of GPU acceleration will facilitate high-throughput alchemical free energy calculations.</p></div></div></div>

Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations

2005 ◽  
Vol 103 (14) ◽  
pp. 1961-1969 ◽  
Author(s):  
Yu Zhou ◽  
Chris Oostenbrink ◽  
Wilfred F. Van Gunsteren ◽  
Wilfred R. Hagen ◽  
Simon W. De Leeuw ◽  
...  
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Relative Stability ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Force Field Parameters

scholarly journals Molecular Environment Specific Atomic Charges Improve Binding Affinity Predictions of SAMPL5 Host-Guest Systems

2021 ◽  
Author(s):  
Duvan Gonzalez ◽  
Luis Macaya ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Binding Affinity ◽  
Free Energy Calculations ◽  
Atomic Charges ◽  
Binding Affinity Prediction ◽  
Energy Calculations ◽  
Affinity Prediction ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

<div> <div> <div> <p>Host-guest systems are widely used in benchmarks as model systems to improve computational methods for absolute binding free energy predictions. Recent advances in sampling algorithms for alchemical free energy calculations and the increase in computational power have made their binding affinity prediction primarily dependent on the quality of the force field. Here, we propose a new methodology to derive the atomic charges of host-guest systems based on QM/MM calculations and the MBIS partitioning of the polarized electron density. A newly developed interface between the OpenMM and ORCA software package provides D-MBIS charges that best represent the guest’s average electrostatic interactions in the hosts or the solvent. The simulation workflow also calculates the average energy required to polarize the guest in the bound and unbound state. Alchemical free energy calculations using the GAFF force field parameters with D-MBIS charges improve the binding affinity prediction of six guests bound to two octa-acid hosts compared to the AM1-BCC charge set after correction with the average energetic polarization cost. This correction results from the difference in the energetic polarization cost between the bound and unbound state and contributes significantly to the binding affinity of anionic guests. </p></div></div></div><div><div><div> </div> </div> </div>

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