TY - JOUR
T1 - Force Field X
T2 - A computational microscope to study genetic variation and organic crystals using theory and experiment
AU - Gogal, Rose A.
AU - Nessler, Aaron J.
AU - Thiel, Andrew C.
AU - Bernabe, Hernan V.
AU - Corrigan Grove, Rae A.
AU - Cousineau, Leah M.
AU - Litman, Jacob M.
AU - Miller, Jacob M.
AU - Qi, Guowei
AU - Speranza, Matthew J.
AU - Tollefson, Mallory R.
AU - Fenn, Timothy D.
AU - Michaelson, Jacob J.
AU - Okada, Okimasa
AU - Piquemal, Jean Philip
AU - Ponder, Jay W.
AU - Shen, Jana
AU - Smith, Richard J.H.
AU - Yang, Wei
AU - Ren, Pengyu
AU - Schnieders, Michael J.
N1 - Publisher Copyright:
© 2024 Author(s).
PY - 2024/7/7
Y1 - 2024/7/7
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85197719500&partnerID=8YFLogxK
U2 - 10.1063/5.0214652
DO - 10.1063/5.0214652
M3 - Article
C2 - 38958156
AN - SCOPUS:85197719500
SN - 0021-9606
VL - 161
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 1
M1 - 012501
ER -