Tutorials

PEFs implemented

All the PEFs implemented, along with examples of input files and scripts to run various types of simulations, are provided in $MBX_HOME/examples/PEFs. If a surface is not there, its usage is not recommended because it is either not tested or not finalized. Example calls with C++, Fortran and Python are located inside each of the corresponding folders.

Please cite the corresponding manuscript whenever using MBX:

• J. Chem. Phys. 159, 054802 (2023)

Please cite the following manuscripts if any of the following PEFs is used:

• MB-pol for water: "h2o" (O H H)
  • J. Chem. Theory Comput. 9, 5395 (2013)
  • J. Chem. Theory Comput. 10, 1599 (2014)
  • J. Chem. Theory Comput. 10, 2906 (2014)
  • J. Chem. Phys. 145, 194504 (2016)
  • Acc. Chem. Res. 49, 1844 (2016)
• MB-nrg PEFs for alkali-metal ions in water: "li+, "na+, "k+, "rb+, "cs+"
  • J. Chem. Phys. 147, 161715 (2017)
  • J. Phys. Chem. A 122, 5811 (2018)
  • J. Phys. Chem. Lett. 10, 406 (2019)
  • J. Chem. Phys. 153, 044306 (2020)
  • J. Chem. Theory Comput. 16, 3055 (2020)
  • J. Phys. Chem. B. 126, 9349 (2022)
• MB-nrg PEFs for halide ions in water: "f-, "cl-, "br-, "i-"
  • J. Chem. Theory Comput. 12, 2698 (2016)
  • J. Chem. Phys. 148, 102321 (2018)
  • J. Comp. Theory. Comput. 15, 2983 (2019)
  • Nat. Chem. 11, 367 (2019)
  • J. Phys. Chem. Lett. 10, 2823 (2019)
  • J. Phys. Chem. A 123, 2843 (2019)
  • Adv. Phys. X 4, 1631212 (2019)
  • J. Chem. Phys. 155, 064502 (2021)
  • J. Phys. Chem. B 126, 8266 (2022)
• MB-nrg PEFs for CO₂ and CO₂/H₂O mixtures: "co2" (C O O)
  • J. Chem. Theory Comput. 16, 2246 (2020)
  • J. Chem. Phys. 156, 104503 (2022)
• MB-nrg PEFs for CH₄ and CH₄/H₂O mixtures: "ch4" (C H H H H)
  • J. Phys. Chem. B 124, 11207 (2020)
  • J. Chem. Phys. 156, 194504 (2022)
• MB-nrg PEF for N₂O₅ in water: "n2o5" (O N N O O O O)
  • J. Chem. Theory Comput. 17, 3931 (2021)