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Describe the bug
The portion of the help text describing GBSA and ALPB:
--alpb SOLVENT [STATE]
analytical linearized Poisson-Boltzmann (ALPB) model,
available solvents are acetone, acetonitrile, aniline, benzaldehyde,
benzene, ch2cl2, chcl3, cs2, dioxane, dmf, dmso, ether, ethylacetate, furane,
hexandecane, hexane, methanol, nitromethane, octanol, woctanol, phenol, toluene,
thf, water.
The solvent input is not case-sensitive. The Gsolv
reference state can be chosen as reference or bar1M (default).
-g, --gbsa SOLVENT [STATE]
generalized born (GB) model with solvent accessable surface (SASA) model,
available solvents are acetone, acetonitrile, benzene (only GFN1-xTB), CH2Cl2,
CHCl3, CS2, DMF (only GFN2-xTB), DMSO, ether, H2O, methanol,
n-hexane (only GFN2-xTB), THF and toluene.
The solvent input is not case-sensitive.
The Gsolv reference state can be chosen as reference or bar1M (default).
Note the last line for each The Gsolv reference state can be chosen as reference or bar1M (default). This seems to imply bar1m is the default reference state. However, running either GBSA or ALPB with no reference state or an unknown reference state will print out in the "Solvation model" section:
Reference state gsolv [1 M gas/solution]
Free energy shift 1.8574E-03 Eh 1.1656E+00 kcal/mol
When running with the reference state explicitly set as bar1M:
Reference state gsolv [1 bar gas/1 M solution]
Free energy shift 4.8887E-03 Eh 3.0677E+00 kcal/mol
So it seems the default reference is really gsolv rather than bar1M.
The text was updated successfully, but these errors were encountered:
Describe the bug
The portion of the help text describing GBSA and ALPB:
Note the last line for each
The Gsolv reference state can be chosen as reference or bar1M (default).
This seems to implybar1m
is the default reference state. However, running either GBSA or ALPB with no reference state or an unknown reference state will print out in the "Solvation model" section:When running with the reference state explicitly set as
bar1M
:So it seems the default reference is really gsolv rather than bar1M.
The text was updated successfully, but these errors were encountered: