3.2. MICRO#
3.2.1. Clusters Extraction#
The MICRO module manages the extraction of microsolvation clusters. It is possible to select N low-energy clusters, each containing M solvent molecules. The value of M can be determined from a previous RDF analysis (using the DATAS module), defined based on the solute-solvent ratio (at a user-specified concentration), or calculated automatically (based on a cutoff distance corresponding to the diameter of the sphere surrounding the solvent molecule). The extraction is performed using the following command:
micro ⟨simbox.trj.xyz⟩ -str N -nsv M
The extraction based on molal concentration C is performed using the command:
micro ⟨simbox.trj.xyz⟩ -str N -bco C
The extraction based on the number S of solvation shells (estimated from the solvent radius) is performed using the command:
micro ⟨simbox.trj.xyz⟩ -str N -sol S
Note
Simply type micro in the terminal and press enter to see the full list of execution options for the module.
3.2.2. Clusters Treatment#
The MICRO module can also perform property calculations based on the microsolvation cluster treatment. This includes the optimization of hydrogen bonds within the clusters, constrained optimization of the entire clusters at the xTB level, and subsequent property evaluation with configurations set by the user. These calculations are executed using the following command:
micro ⟨solute.trj.xyz⟩ -opt -hbd -key “keywords”
Note
Simply type micro in the terminal and press enter to see the full list of execution options for the module.
3.2.3. Execution Options#
micro ⟨trajectory.trj.xyz⟩ [⟨-options⟩]
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MICROSOLVATION CLUSTERS EXTRACTION [-ce]
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auto : Execute an automated microsolvation clusterization from simulation files. [-ms]
» Description
bCon = 1 mol·kg⁻¹ (for setting the number of solvent molecules)
Nstr = 1% of trajectory structures (1000 min, 10000 max)
cTRJ = All production steps
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-str = Number of clustered structures selected trajectory. [Default: 1000] [Int.] [-nc]⁽*⁾
-nsv = Number of solvent molecules in the clustering process. [Default: 0] [Int.] [-ns]⁽*⁾
-sol = Number of solvent layers in the clustering process. [Default: 1] [Int.] [-nl]⁽*⁾
-bco = Molal conc. of the microsolvation cluster (in mol·kg⁻¹). [Default: 0.0] [Real] [-bc]⁽*⁾
-cfg = Nº of MD equilibration steps [:Nº of MD production steps]. [Default: 0:0] [Auto] [-ct]⁽*⁾
-chr = Value of microsolvated solute charge. [Default: 0] [Int.] [-ch]⁽*⁾
-mlt = Value of microsolvated solute multiplicity. [Default: 1] [Int.] [-ml]⁽*⁾
-prs = Value of simulation pressure (in bar). [Default: 1.0] [Real] [-pr]⁽*⁾
-tmp = Value of simulation temperature (in K). [Default: 298] [Real] [-tp]⁽*⁾
-svt = Solvent to be used in ALPB solvation model. [Default: Auto] [Text] [-sv]⁽*⁾
-rtn : Retain the original orientation of the clusters. [Default: No] [-rt]⁽*⁾
-psv : Preserve the original trajectory file. [Default: No] [-pv]⁽*⁾
-for : Execute in forced mode. [Default: No] [-fm]⁽*⁾
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-prc = Number of parallel CPU processes to run. [Default: 8] [-pc]⁽*⁾
-mem = Amount of memmory to be used (in GB). [Default: 16] [-mm]⁽*⁾
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micro ⟨solute.trj.xyz⟩ [⟨-options⟩]
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MICROSOLVATION CLUSTERS TREATMENT [-ct]
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-opt : Optimize microsolvation cluster structures (FCA procedure).[Default: No] [-op]
-hbd : Optimize hydrogen bonding in the microsolvation cavity. [Default: No] [-hb]
-key = “List of keywords” for final calculation (with ORCA). [Default: M062X 6-311+G(d)] [-kw]⁽*⁾
-for : Execute in forced mode. [Default: No] [-fm]
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-prc = Number of parallel CPU processes to run. [Default: 8] [-pc]⁽*⁾
-mem = Amount of memmory to be used (in GB). [Default: 16] [-mm]⁽*⁾
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⁽*⁾ Configurable options in automated mode.
3.2.4. Quickstart Examples#
Example #1: Extracting clusters from a simulation with ORCA
Example #2: Extracting clusters from a simulation with GROMACS