Efficient Solvation Free Energy Calculations of Amino Acid Analogs by Expanded Ensemble Molecular Simulation

2011 ◽  
Vol 7 (5) ◽  
pp. 1394-1403 ◽  
Author(s):  
Andrew S. Paluch ◽  
Jindal K. Shah ◽  
Edward J. Maginn
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Molecular Simulation ◽  
Solvation Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Amino Acid Analogs ◽  
Expanded Ensemble

scholarly journals Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages

2018 ◽  
Vol 14 (11) ◽  
pp. 5567-5582 ◽  
Author(s):  
Hannes H. Loeffler ◽  
Stefano Bosisio ◽  
Guilherme Duarte Ramos Matos ◽  
Donghyuk Suh ◽  
Benoit Roux ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Simulation ◽  
Simulation Software ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Software Packages

Performing solvation free energy calculations in LAMMPS using the decoupling approach

2020 ◽  
Vol 34 (6) ◽  
pp. 641-646
Author(s):  
Vikram Khanna ◽  
Jacob I. Monroe ◽  
Michael F. Doherty ◽  
Baron Peters
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Decoupling Approach

scholarly journals Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

2018 ◽  
Author(s):  
Hannes H. Loeffler ◽  
Stefano Bosisio ◽  
Guilherme Duarte Ramos Matos ◽  
Donghyuk Suh ◽  
Benoît Roux ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Simulation ◽  
Simulation Software ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Small Organic Molecules ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Attention To Detail ◽  
Alchemical Free Energy Calculations

<div> <div> <div> <p>Alchemical free energy calculations are an increasingly important modern simulation technique. Contemporary molecular simulation software such as AMBER, CHARMM, GROMACS and SOMD include support for the method. Implementation details vary among those codes but users expect reliability and reproducibility, i.e. for a given molec- ular model and set of forcefield parameters, comparable free energy should be obtained within statistical bounds regardless of the code used. Relative alchemical free energy (RAFE) simulation is increasingly used to support molecule discovery projects, yet the reproducibility of the methodology has been less well tested than its absolute counter- part. Here we present RAFE calculations of hydration free energies for a set of small organic molecules and demonstrate that free energies can be reproduced to within about 0.2 kcal/mol with aforementioned codes. Achieving this level of reproducibility requires considerable attention to detail and package–specific simulation protocols, and no uni- versally applicable protocol emerges. The benchmarks and protocols reported here should be useful for the community to validate new and future versions of software for free energy calculations.</p></div></div></div>

scholarly journals The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

2019 ◽  
Author(s):  
Andrea Rizzi ◽  
Travis Jensen ◽  
David R. Slochower ◽  
Matteo Aldeghi ◽  
Vytautas Gapsys ◽  
...  
Keyword(s):  
Free Energy ◽  
Convergence Rates ◽  
Binding Free Energy ◽  
Potential Of Mean Force ◽  
Free Energy Calculations ◽  
Energy Estimates ◽  
Initial Population ◽  
Energy Calculations ◽  
Partial Charges ◽  
Expanded Ensemble

AbstractApproaches for computing small molecule binding free energies based on molecular simulations are now regularly being employed by academic and industry practitioners to study receptor-ligand systems and prioritize the synthesis of small molecules for ligand design. Given the variety of methods and implementations available, it is natural to ask how the convergence rates and final predictions of these methods compare. In this study, we describe the concept and results for the SAMPL6 SAMPLing challenge, the first challenge from the SAMPL series focusing on the assessment of convergence properties and reproducibility of binding free energy methodologies. We provided parameter files, partial charges, and multiple initial geometries for two octa-acid (OA) and one cucurbit[8]uril (CB8) host-guest systems. Participants submitted binding free energy predictions as a function of the number of force and energy evaluations for seven different alchemical and physical-pathway (i.e., potential of mean force and weighted ensemble of trajectories) methodologies implemented with the GROMACS, AMBER, NAMD, or OpenMM simulation engines. To rank the methods, we developed an efficiency statistic based on bias and variance of the free energy estimates. For the two small OA binders, the free energy estimates computed with alchemical and potential of mean force approaches show relatively similar variance and bias as a function of the number of energy/force evaluations, with the attach-pull-release (APR), GROMACS expanded ensemble, and NAMD double decoupling submissions obtaining the greatest efficiency. The differences between the methods increase when analyzing the CB8-quinine system, where both the guest size and correlation times for system dynamics are greater. For this system, nonequilibrium switching (GROMACS/NS-DS/SB) obtained the overall highest efficiency. Surprisingly, the results suggest that specifying force field parameters and partial charges is insufficient to generally ensure reproducibility, and we observe differences between seemingly converged predictions ranging approximately from 0.3 to 1.0 kcal/mol, even with almost identical simulations parameters and system setup (e.g., Lennard-Jones cutoff, ionic composition). Further work will be required to completely identify the exact source of these discrepancies. Among the conclusions emerging from the data, we found that Hamiltonian replica exchange—while displaying very small variance—can be affected by a slowly-decaying bias that depends on the initial population of the replicas, that bidirectional estimators are significantly more efficient than unidirectional estimators for nonequilibrium free energy calculations for systems considered, and that the Berendsen barostat introduces non-negligible artifacts in expanded ensemble simulations.

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