3.3. GCALC#
3.3.1. Clusters Treatment#
The GCALC module manages the H-bond clusters treatment. After extraction with MICRO module, the selected clusters are saved in a file solute.trj.xyz. This module are executed in two steps. In the first, all clusters present in the input file are characterized, aiming to select several C clusters with the lowest energy, with the command:
gcalc ⟨solute.trj.xyz⟩ -ini -max C
In the second step, the C clusters are prepared for optimization and the Gibbs free energy extrapolation, considering one of the treatment options to remove any imaginary frequencies:
gcalc ⟨solute.trj.xyz⟩ -opt -max C
In this step, the input files are saved in a separate jobrunning folder.
Note
Simply type gcalc in the terminal and press enter to see the full list of execution options for the module.
3.3.2. Execution Options#
gcalc ⟨solute.trj.xyz⟩ [⟨-options⟩]
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auto : Execute an automated microsolvation optimization. [-ga]
» NOTE: this option is recommended in queue systems.
» HINT: -auto [starts processing 100 clusters]
: -auto N [starts processing N clusters]
: -auto +M [add M clusters to the previous analysis]
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STEPS CONTROL [-sc]
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● Stage #1: Clusters Characterization [-s1]⁽▪⁾
-ini : Execute clusters characterization and selection. [Default: Auto] [-ic]
Characterization for structures selection.
Procedure performed at xTB-GFF level.
● Stage #2: Clusters Treatment [-s2]⁽▪⁾
-opt : Optimization and free energy calculation. (FSA|FCA) [Default: FCA] [-op]
Calculation after structures selection.
Procedure performed at xTB-GFN2 level combined with DFT.
» FSA: [F]ull [S]olutes [A]ccommodated geometry (with SPH).¹ «xTB level»
» FCA: [F]ull [C]luster [A]ccommodated geometry (with SPH).¹ «xTB level»
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ADITIONAL OPTIONS [-ao]
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● Selection Options
-max = Maximum number of structures into energy window. [Default: 100] [-nw]⁽*⁾
-add = Add M clusters to GFE procedure from INI step. [Default: Not defined] [-ad]⁽*⁾
● System Options
-chr = Value of microsolvated solute charge. [Default: Auto] [-ch]⁽*⁾
-mlt = Value of microsolvated solute multiplicity. [Default: Auto] [-ml]⁽*⁾
-prs = Pressure for thermochemistry calculation (in atm). [Default: Auto] [-ps]⁽*⁾
-tmp = Temperature for thermochemistry calculation (in K). [Default: Auto] [-tp]⁽*⁾
● Solvation Options
-svt = Solvent type (for ALPB/CPCM solvation method). [Default: Auto] [-sv]⁽*⁾
-nis = No implicit solvation. [Default: None] [-ni]⁽*⁾
● Configuration Options
-prc = Number of parallel CPU processes to run. [Default: 8] [-pc]⁽*⁾
-mem = Amount of memmory to be used (in GB). [Default: 16] [-mm]⁽*⁾
● Additional Options
-key = “List of keywords” (for ONIOM program). [Default: None] [-kw]⁽*⁾
-fcc = Final concentration after compression. [Default: 1.0 mol·kg⁻¹] [-fc]⁽*⁾
-hbd : Include H-bonds at extrapolation (for ORCA final step). [Default: No] [-nm]⁽*⁾
-nmr : Config. for NMR calculation (for ORCA final step). [Default: No] [-nm]⁽*⁾
-for : Force reexecution stages. [Default: No] [-fm]⁽*⁾
-fil : Filter high energy clusters (above 100.0 kcal·mol⁻¹). [Default: No] [-fi]⁽*⁾
+ ----------------------------------------------------------
-dat : Extract data for selected stage. [Default: No] [-dt]⁽*⁾
-plt : Plot extracted data. [Default: No] [-pd]⁽*⁾
-bak : Save generated graphs (without iterative interface). [Default: No] [-bk]
+ ----------------------------------------------------------
-exc = List of structural clusters to exclude. (inp) [i,j,k,...] [Default: None] [-ex]⁽†⁾
-clr = List of optimized clusters to clean. (out) [i,j,k,...] [Default: None] [-cl]⁽‡⁾
+ ----------------------------------------------------------
-del = Delete specified previous optimization. [Default: No] [-dc]
-ext = Extract specified previous calculation. [Default: No] [-ec]
-ren = Rename specified previous description. “DSC” / [OLD:NEW] [Default: No] [-rn]
-chk : Check all previous calculations. (= spec. to extract) [Default: No] [-ck]
-log : Summary of performed calculations. [Default: No] [-lg]
+ ----------------------------------------------------------
-out = Force reading specified ONIOM output file. [Default: No] [-of]
: Force reading default ONIOM output file. [Default: No] [-of]
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Total CPUs: 12 (max. MPI-procs.) :: System Memory: 5 GB
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⁽*⁾ Configurable options in automated mode.
⁽▪⁾ Try “-sN” to view stage N only.
⁽†⁾ The “ith” cluster identified from trj.xyz input file.
⁽‡⁾ The “ith” cluster identified through graphical analysis.
⁽¹⁾ SPH = Single Point Hessian.
⁽²⁾ CHM = Conventional Hessiam Method.
3.3.3. Quickstart Examples#
Example #1: Treating clusters from a simulation with GROMACS