Database¶
mdinterface ships a built-in database of common species with pre-defined force-field parameters. All entries are importable from mdinterface.database.
Metals¶
from mdinterface.database import Metal111
gold = Metal111("Au")
silver = Metal111("Ag")
platinum = Metal111("Pt")
copper = Metal111("Cu")
Metal111 generates an FCC (111) surface slab. The element symbol selects the lattice parameter and Lennard-Jones parameters.
Water models¶
from mdinterface.database import Water
water_spce = Water(model="ewald") # modified tip3p model
water_tip4p = Water(model="spce") # SPC/E water
Ions¶
from mdinterface.database import Ion
na = Ion("Na", ffield="Cheatham")
cl = Ion("Cl", ffield="Cheatham")
li = Ion("Li", ffield="Cheatham")
k = Ion("K", ffield="Cheatham")
Currently, the following force field parameters for monovalent ions have been implemented:
- Aqvist : J. Phys. Chem. B 2008, https://pubs.acs.org/doi/10.1021/jp8001614,
- Jorgensen: J. Chem. Theory Comput. 2006, https://pubs.acs.org/doi/10.1021/ct600252r
- Cheatham : J. Phys. Chem. B 2008, https://pubs.acs.org/doi/10.1021/jp8001614
- Sengupta : J. Chem. Inf. Model. 2021, https://pubs.acs.org/doi/10.1021/acs.jcim.0c01390
- Dang : J. Chem. Phys. 1992/1994
- OPLS-AA : J. Chem. Theory Comput. 2009, https://pubs.acs.org/doi/10.1021/ct900009a
Special ion species also available:
If the parameter set you are looking for are not present, you can always create a Specie explicitly:
Noble gases¶
from mdinterface.database import Neon, Argon, Krypton, Xenon, NobleGas
ar = Argon()
xe = Xenon()
# or generically:
gas = NobleGas("Kr")