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. Execution Options#
micro ⟨trajectory.trj.xyz⟩ [⟨-options⟩]
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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.] [-str]⁽*⁾
-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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⁽*⁾ Configurable options in automated mode.
3.2.3. Quickstart Examples#
Example #1: Extracting clusters from a simulation with ORCA
Example #2: Extracting clusters from a simulation with GROMACS