Implicit Solvation¶
In this chapter, all neccessary information will be given in order to use the implicit solvent model ALPB in xTB calculations. Parameterized solvents and available grids are given as well.
Contents
General command-line control¶
Note
The ALPB solvation model is implemented in version 6.3.3 or newer, use --gbsa
in older versions instead.
The analytical linearized Poisson-Boltzmann (ALPB) model is envoked with the flag --alpb [Solvent]
.
As an example the single point calculation employing the ALPB model for solvation in water would be started by
> xtb coord --alpb water
As an example the energy printout of a singlepoint calculation of a H₂O molecule in implicit water is given.
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -5.080052453799 Eh ::
:: total w/o Gsasa/hb -5.072629830168 Eh ::
:: gradient norm 0.004391355361 Eh/α ::
:: HOMO-LUMO gap 14.784541887474 eV ::
::.................................................::
:: SCC energy -5.113963912352 Eh ::
:: -> isotropic ES 0.042951967946 Eh ::
:: -> anisotropic ES -0.000414697277 Eh ::
:: -> anisotropic XC -0.000390138125 Eh ::
:: -> dispersion -0.000131341861 Eh ::
:: -> Gsolv -0.011759733450 Eh ::
:: -> Gborn -0.004337109820 Eh ::
:: -> Gsasa 0.000220003644 Eh ::
:: -> Ghb -0.009500070401 Eh ::
:: -> Gshift 0.001857443127 Eh ::
:: repulsion energy 0.033911458523 Eh ::
:: add. restraining 0.000000000000 Eh ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
The solvation free energy is printed as Gsolv
and is also added
to all total energy printouts.
Optimizing a geometry with the ALPB model can be done with the following input
> xtb coord --opt --alpb water
The order of the flags can be altered and the input
is not case sensitive.
Like in a optimization without ALPB the optimized coordinates are
written to a new file (xtbopt.coord
).
In General the ALPB can be used in combination with all available run types
implemented in the xtb.
Parameterized Solvents¶
The ALPB model is parameterized for the Hamiltonian of GFN1-xTB, GFN2-xTB, and the GFN-FF, but not for GFN0-xTB. For the GFN1-xTB and GFN2-xTB Hamltonians also a generalized Born (GB) model with surface area (SA) contributions, dubbed GBSA is available. Here is a list of the available solvents.
solvents |
GFN1(ALPB) |
GFN1(GBSA) |
GFN2(ALPB) |
GFN2(GBSA) |
GFN-FF |
---|---|---|---|---|---|
Acetone |
x |
x |
x |
x |
x |
Acetonitrile |
x |
x |
x |
x |
x |
Aniline |
x |
x |
x |
||
Benzaldehyde |
x |
x |
x |
||
Benzene |
x |
x |
x |
x |
x |
CH₂Cl₂ |
x |
x |
x |
x |
x |
CHCl₃ |
x |
x |
x |
x |
x |
CS₂ |
x |
x |
x |
x |
x |
Dioxane |
x |
x |
x |
||
DMF |
x |
x |
x |
||
DMSO |
x |
x |
x |
x |
x |
Ether |
x |
x |
x |
x |
x |
Ethylacetate |
x |
x |
x |
||
Furane |
x |
x |
x |
||
Hexadecane |
x |
x |
x |
||
Hexane |
x |
x |
x |
x |
|
Methanol |
x |
x |
|||
Nitromethane |
x |
x |
x |
||
Octanol |
x |
x |
x |
||
Octanol (wet) |
x |
x |
x |
||
Phenol |
x |
x |
x |
||
Toluene |
x |
x |
x |
x |
x |
THF |
x |
x |
x |
x |
x |
Water (H₂O) |
x |
x |
x |
x |
x |
To get the legacy GBSA model setup a detailed input with
$gbsa
kernel=still
and invoke the program with the --gbsa
flag instead of the --alpb
flag.
Available Grids¶
Different Lebedev grids for the calculation of the SASA term are
implemented in xtb
. The grids are independent of the used GFNn method
and are set in the detailed input as
$gbsa
gbsagrid=tight
The default grid level is normal
.
The available grid levels are given in the table below
with the corresponding number of gridpoints.
Gridlevel |
Gridpoints |
---|---|
normal |
230 |
tight |
974 |
verytight |
2030 |
extreme |
5810 |
Larger grids increase the computation time and reduce numerical noise in the energy. They may help to converge geometry optimizations with ALPB for large molecules which would otherwise not converge due to numerical noise.
Reference States¶
The default reference state option is bar1M
which should not
be changed for normal production runs.
In order to compare the solvation free energy with
solvation free energies from COSMO-RS the reference state can be set to reference
which corresponds
to the same reference
option as in COSMO-RS. This could be done with
> xtb coord --opt --alpb water reference
Extended Functionality¶
Solvent Accessable Surface Area¶
Note
feature implemented in version 6.2
To get more insights and diagnostics for a ALPB calculation the Born radii and the solvent accessable surface area can be printed by toggling the property-printout with
$write
gbsa=true
The printout for a branched octane isomer using ALPB(Water) looks like
* generalized Born model for continuum solvation
# Z Born rad/ŠSASA/Ų H-bond
1 6 C 3.761 0.000 0.000
2 6 C 3.761 0.000 0.000
3 6 C 2.741 1.820 -0.000
4 6 C 2.741 1.839 -0.000
5 6 C 2.741 1.817 -0.000
6 6 C 2.741 1.820 -0.000
7 6 C 2.741 1.839 -0.000
8 6 C 2.741 1.817 -0.000
9 1 H 2.136 11.404 -0.015
10 1 H 2.130 12.571 -0.017
11 1 H 2.098 14.966 -0.020
12 1 H 2.130 12.563 -0.017
13 1 H 2.098 14.979 -0.020
14 1 H 2.136 11.403 -0.015
15 1 H 2.136 11.412 -0.015
16 1 H 2.130 12.524 -0.017
17 1 H 2.098 14.948 -0.020
18 1 H 2.136 11.404 -0.015
19 1 H 2.130 12.571 -0.017
20 1 H 2.098 14.966 -0.020
21 1 H 2.130 12.563 -0.017
22 1 H 2.098 14.979 -0.020
23 1 H 2.136 11.403 -0.015
24 1 H 2.136 11.412 -0.015
25 1 H 2.130 12.524 -0.017
26 1 H 2.098 14.948 -0.020
total SASA / Ų : 244.491
The quartary carbon atoms are shown with no solvent accessable surface area, which means they are completely buried in the molecule leading to large Born radii.