| layout | default |
|---|---|
| title | QCG Example 4 |
| parent | QCG Examples |
| grand_parent | Examples and Guides |
| nav_order | 4 |
| toc | false |
| summary | An example for the calculation of Solvation Free Energies with QCG. |
| permalink | /page/examples/qcg/example_4.html |
{: .no_toc }
{{ page.summary }} {: .fs-6 .fw-300 }
The solvation free energy can be computed for any solute-solvent combination with QCG.
Again, only input geometries are required.
Let’s consider 1-pentanol in benzene.
We provide the input coordinates pentanol.xyz and benzene.coord.
The following call will initiate the solvation free energy computation.
{: .text-justify }
command
{{ site.data.icons.codefile }} pentanol.xyz
{{ site.data. icons.codefile }} benzene.coord
{{ site.data. icons.checkfile }} output
C 1.1956067224 0.3810439760 0.2749699821 C 2.6993267582 0.1988054806 0.4398058012 C 3.3048739621 -0.5930561241 -0.7170407712 C 4.8104223372 -0.7810968097 -0.5556226318 C 5.4141490570 -1.5692919510 -1.7184358828 O 6.7925871816 -1.8090235819 -1.5591217978 H 0.7847307317 0.9460737154 1.1083269558 H 0.6967141904 -0.5847813396 0.2356859339 H 0.9746565928 0.9171147501 -0.6455272552 H 2.9009463902 -0.3234896023 1.3776341886 H 3.1790981167 1.1786519338 0.4972352731 H 3.1045811920 -0.0710584163 -1.6560239285 H 2.8240160617 -1.5719984791 -0.7751608993 H 5.0195701758 -1.3132022816 0.3749761863 H 5.2956555541 0.1982438034 -0.4961001357 H 5.2241018357 -1.0388860571 -2.6640512701 H 4.9541986817 -2.5581683607 -1.7828096756 H 7.2421309110 -0.9635515651 -1.4497510164 {% endcapture %} {% include codecell.html content=struc_file style="font-size:10px" %}
Cite work conducted with this code as
P. Pracht, F. Bohle, S. Grimme, PCCP, 2020, 22, 7169-7192.
and S. Grimme, JCTC, 2019, 15, 2847-2862.
with help from: C.Bannwarth, F.Bohle, S.Ehlert, S.Grimme, C. Plett, P.Pracht, S. Spicher
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Command line input:
crest pentanol.xyz --qcg benzene.coord -nsolv 25 -T 12 -gsolv -nclus 4 -fscal 0.65 -gbsa benzene
Solute-file: pentanol.xyz Solvent-file: benzene.coord -T 12 (CPUs/Threads selected) Use of GFN-FF for ensemble search requested. Use of GFN-FF for frequency computation requested. --gbsa benzene : implicit solvation -mdtime 10 (MD length in ps)
| ======================================== |
|---|
| Q C G |
| ---------------- |
| Quantum Cluster Growth |
| University of Bonn, MCTC |
| ======================================== |
| S. Grimme, S. Spicher, C.Plett, unpublished. |
QCG: Calculation of delta G_solv Ensemble generated via CREST
input parameters solute : pentanol.xyz charge : 0 uhf : 0 solvent : benzene.coord
Solvation model : benzene xtb opt level : normal System temperature [K] : 298.0 RRHO scaling factor : 0.65
Solute geometry molecular radius (Bohr1): 6.52 molecular area (Bohr2): 651.12 molecular volume (Bohr3): 1159.46 Solvent geometry molecular radius (Bohr1): 6.06 molecular area (Bohr2): 516.08 molecular volume (Bohr3): 931.74
radius of solute : 10.51 radius of solvent : 9.77
Geometry successfully optimized. Generating LMOs for solute Total Energy of solute: -20.8872146 Eh
Geometry successfully optimized. Generating LMOs for solvent Total energy of solvent: -15.8796407 Eh
__________________ Solute Cluster Generation _____________________
[...]
[...]
_________________ Solvent Cluster Generation _____________________
Method for CFF: GFN2-xTB
CUT-FREEZE-FILL Algorithm to generate reference solvent cluster now adding solvents to fill cluster... Size Cluster E /Eh De/kcal Detot/kcal Opt
adding solvent is repulsive for cluster: 1 previous cluster taken... 26 2 -413.211286 -2.24 -2.24 tight 26 3 -413.210426 -3.44 -3.44 tight 26 4 -413.216554 -7.37 -7.37 tight
volume filled Starting optimizations + SP of structures 4 jobs to do.
done.
Cluster E /Eh Density Efix R av/act. Surface Opt 1 -397.332086 1.067 0.000 0.0 0.0 5955.5 tight 2 -397.318544 1.060 0.000 0.0 0.0 6373.5 tight 3 -397.317717 1.057 0.000 0.0 0.0 6591.9 tight 4 -397.323610 1.058 0.000 0.0 0.0 6433.2 tight
Boltz. averaged energy of final cluster: G /Eh : -397.33208567 T*S /kcal : -0.001
Solvent cluster generation finished. Results can be found in solvent_cluster directory Structures on file 'crest_ensemble.xyz' Energies on file 'cluster_energy.dat' Population on file 'population.dat'
Method for CFF: GFN-FF SOLUTE MOLECULE Starting reoptimizations + Frequency computation of ensemble 1 jobs to do.
done. SOLUTE CLUSTER Starting reoptimizations + Frequency computation of ensemble 4 jobs to do.
done. SOLVENT CLUSTER Starting reoptimizations + Frequency computation of ensemble 4 jobs to do.
done.
Solute Gas properties
[kcal/mol] [ cal/mol/K ] [kcal/mol]
108.59 20.37 27.20 39.32 82.68
Solute cluster properties
[kcal/mol] [ cal/mol/K ] [kcal/mol]
1 1794.49 762.14 44.60 48.69 1539.44 2 1794.49 763.02 44.55 48.69 1539.19 3 1794.21 766.70 44.64 48.69 1537.80 4 1794.06 761.65 44.61 48.69 1539.16
Solvent cluster properties
[kcal/mol] [ cal/mol/K ] [kcal/mol]
1 1683.97 718.09 44.20 48.55 1442.21 2 1683.88 721.14 44.26 48.55 1441.20 3 1683.17 730.73 44.55 48.55 1437.54 4 1683.61 722.85 44.32 48.55 1440.40
_________________________ Evaluation ____________________________
Gsolv and Hsolv ref. state: [1 M gas/solution] G_solv (incl.RRHO) = 3.65 kcal/mol H_solv (incl.RRHO) = -7.64 kcal/mol
Gsolv and Hsolv ref. state: [1 M gas/solution] G_solv (incl.RRHO) = 1.75 kcal/mol H_solv (incl.RRHO) = -9.54 kcal/mol
Solvation free energies with scaled translational and rotational degrees of freedom: Gsolv (scaling) >> -16.93 (0.05) << >> -15.95 (0.10) << >> -14.97 (0.15) << >> -13.98 (0.20) << >> -13.00 (0.25) << >> -12.01 (0.30) << >> -11.03 (0.35) << >> -10.05 (0.40) << >> -9.06 (0.45) << >> -8.08 (0.50) << >> -7.10 (0.55) << >> -6.11 (0.60) << >> -5.13 (0.65) << >> -4.15 (0.70) << >> -3.16 (0.75) << >> -2.18 (0.80) << >> -1.20 (0.85) << >> -0.21 (0.90) << >> 0.77 (0.95) << >> 1.75 (1.00) <<
================================================== | Gsolv with SCALED RRHO contributions: 0.75 | | [1 bar gas/ 1 M solution] | | | | G_solv (incl.RRHO)+dV(T)= -5.13 kcal/mol |
test MD wall time : 0h : 0m :13s
MTD wall time : 0h :39m : 3s
multilevel OPT wall time : 0h :46m :35s
MD wall time : 5h :23m :24s
CFF wall time : 0h :16m : 7s
Frequencies wall time : 0h : 1m :48s
Overall wall time : 7h : 7m :12s
CREST terminated normally. {% endcapture %} {% include codecell.html content=struc_file style="font-size:10px" %}
The call will cause the grow algorithm to start with subsequent ensemble generation.
In addition to the solute-solvent ensemble also a pure solvent ensemble will be
created from the solute-solvent ensemble. These reference clusters can be found in
the directory solvent_ensemble.
{: .text-justify }
{% include note.html content="The reference ensemble is created per default with the CFF algorithm. This can be switched off by --nocff. Then, the second ensemble is generated similar to the solute-solvent cluster but without the solvent. However, this procedure is usually computationally more demanding and yields worse results. Therefore, it is recommended to always use the CFF algorithm." %}
The number of clusters that are considered for the solvation free energy were set
to 4 with --nclus 4. This reduces the computational costs as only four reference
clusters are computed and only 4 frequency calculations are performed per ensemble.
Therefore, only the 4 energetically best clusters are written to final_ensemble.xyz.
{: .text-justify }
The solvation free energy for 1-pentanol in benzene at the given scaling factor can be read from the output. Additionally, the results for some other scaling factors are also provided. {: .text-justify }
{% include note.html content="The scaling factor of the translational and rotational entropy is empirically determined to be 0.75. As different solvents will quench these parts differently, also the scaling factor has to be adjusted. For example, 0.65 yielded better solvation free energies in case of benzene as solvent." %}
{% include important.html content="As finding an almost complete ensemble for a cluster containing many molecules is only feasible with a large computational effort, QCG suffers from a statistical error. As this is often no problem for many uses of the ensemble, the solvation free energy is in a way sensitive to the completeness. It is recommended to repeat the solvation free energy computation a few times and average the results to reduce this uncertainty." %}