Journal article
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
The Journal of chemical physics, Vol.161(1), 012501
07/07/2024
DOI: 10.1063/5.0214652
PMCID: PMC11223778
PMID: 38958156
Abstract
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
Details
- Title: Subtitle
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
- Creators
- Rose A Gogal - University of IowaAaron J Nessler - University of IowaAndrew C Thiel - University of IowaHernan V Bernabe - University of IowaRae A Corrigan Grove - Los Alamos National LaboratoryLeah M Cousineau - University of IowaJacob M Litman - University of IowaJacob M Miller - University of IowaGuowei Qi - University of IowaMatthew J Speranza - University of IowaMallory R Tollefson - University of IowaTimothy D FennJacob J Michaelson - University of IowaOkimasa OkadaJean-Philip Piquemal - Sorbonne UniversitéJay W Ponder - Washington University in St. LouisJana Shen - University of BaltimoreRichard J H Smith - University of IowaWei Yang - Florida State UniversityPengyu Ren - The University of Texas at AustinMichael J Schnieders - University of Iowa
- Resource Type
- Journal article
- Publication Details
- The Journal of chemical physics, Vol.161(1), 012501
- DOI
- 10.1063/5.0214652
- PMID
- 38958156
- PMCID
- PMC11223778
- NLM abbreviation
- J Chem Phys
- ISSN
- 1089-7690
- eISSN
- 1089-7690
- Language
- English
- Date published
- 07/07/2024
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Communication Sciences and Disorders; Molecular Physiology and Biophysics; Psychiatry; Iowa Technology Institute; Anatomy and Cell Biology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Biochemistry and Molecular Biology; Chemical and Biochemical Engineering; Otolaryngology; Internal Medicine
- Record Identifier
- 9984650360102771
Metrics
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