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Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach
Kepa K Burusco1, Neil J Bruce1,2, Irfan Alibay1
1Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
|September 30, 2015
Summary
This study introduces swarm-enhanced sampling thermodynamic integration (sesTI), a novel computational method. sesTI improves the accuracy of free energy simulations for complex chemical transformations by enhancing sampling efficiency.
Area of Science:
- Computational chemistry
- Molecular dynamics simulations
- Chemical thermodynamics
Background:
- Free energy simulations are crucial for modeling condensed-phase chemical changes.
- Sampling kinetically distinct substates remains a significant challenge for current simulation methods.
Purpose of the Study:
- To develop and validate a novel computational approach combining thermodynamic integration (TI) with swarm-enhanced sampling molecular dynamics (sesMD).
- To address the limitations of traditional TI methods in sampling complex energy landscapes.
Main Methods:
- Integration of thermodynamic integration (TI) with swarm-enhanced sampling molecular dynamics (sesMD), termed sesTI.
- Alchemical free energy calculations for alkane transformations in solution.
- Comparison with multiple independent trajectory TI (IT-TI) methods.
Main Results:
- Traditional IT-TI methods showed increasing inaccuracy with higher intramolecular barriers.
- sesTI calculations demonstrated improved sampling efficiency and accuracy in free energy difference computations.
- The sesTI approach proved effective even for systems with high energy barriers.
Conclusions:
- The sesTI method offers a promising solution for accurately modeling chemical changes in systems with slow conformational exchange.
- This approach enhances the reliability of free energy simulations for complex chemical processes.
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