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Published on: March 3, 2021
Systematic fragmentation method and the effective fragment potential: an efficient method for capturing molecular
Jonathan M Mullin1, Luke B Roskop, Spencer R Pruitt
1Iowa State University, Ames Laboratory, Ames, Iowa, USA.
The Journal of Physical Chemistry. A
|September 11, 2009
Summary
The systematic fragmentation method (SFM) reduces computational cost for large molecules. Employing effective fragment potentials (EFP) accurately captures nonbonded interactions, making SFM a viable computational chemistry tool.
Area of Science:
- Computational Chemistry
- Quantum Chemistry
- Molecular Modeling
Background:
- Systematic fragmentation method (SFM) reduces computational cost for large molecular systems.
- Accurate calculation of nonbonded interactions is crucial for maintaining accuracy in fragmented methods.
- High computational cost of nonbonded interactions can be a bottleneck in large-scale molecular simulations.
Purpose of the Study:
- To explore the efficacy of the effective fragment potential (EFP) method for calculating nonbonded interactions within the SFM framework.
- To assess the accuracy of EFP in capturing nonbonded interactions compared to traditional ab initio methods.
- To demonstrate the viability of combining SFM with EFP for accurate and efficient molecular modeling.
Main Methods:
- Systematic fragmentation method (SFM) to divide large molecular systems.
- Effective fragment potential (EFP) method to compute nonbonded interactions between fragments.
- Comparison of EFP results with ab initio methods for various molecular systems.
Main Results:
- EFP accurately captures nonbonded interactions, comparable to second-order perturbation theory, especially beyond 2.7 Å.
- SFM combined with EFP achieved a 0.2 kcal/mol error for retinal cis-trans isomerization.
- A mean error of 1.0 kcal/mol was observed for alpha-helix isomerization energies using SFM with EFP.
Conclusions:
- The EFP method is a viable and accurate approach for evaluating nonbonded interactions in the SFM.
- Combining SFM with EFP significantly reduces computational cost while maintaining high accuracy for molecular simulations.
- This approach offers a promising computational strategy for studying large molecular systems and their properties.
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