MSRUN

3.1. MSRUN#

3.1.1. Microsolvation Execution#

The MSRUN module manages the entire execution of microsolvation treatment. The module can be run from the main program or directly from the command:

msrun ⟨input.trj.xyz⟩ [⟨-options⟩]

where input.trj.xyz can be the file simbox.trj.xyz (from extracted trajectory file with TRAJS module, which corresponds to the complete procedure by default), or the file solute.trj.xyz (from extracted clusters file with MICRO module, in which the partial procedure is executed, without MICRO reexecution). The settings provided via -options make it possible to adjust the execution of the MICRO, BONDS/GCALC, QUEUE, and ONIOM modules independently.

Note

Simply type msrun in the terminal and press enter to see the full list of execution options for the module.

3.1.2. Execution Options#

msrun ⟨simbox.trj.xyz⟩ [⟨-options⟩]⁽ᵃ⁾

or

msrun ⟨solute.trj.xyz⟩ [⟨-options⟩]⁽ᵇ⁾

  -------------------------------------------------------------------------------------------------
    -auto : Execute an automated microsolvation optimization.                                      [-ac]
          + ----------------------------------------------------------
     -mic = MICRO module configuration. [ Ex.: -mc "-str 1000 -bco 1.0" ]                          [-mc]⁽*⁾
     -bnd = BONDS module configuration. [ Ex.: -bd "-ini -opt -max 100 -fco" ]                     [-bd]⁽*⁾
     -gcc = GCALC module configuration. [ Ex.: -gc "-ini -opt -max 100 -fca" ]                     [-gc]⁽*⁾
     -que = QUEUE module configuration. [ Ex.: -qc "-key “#ONIOM(M062X/6-311+G(d,p):xTB)...”" ]    [-qc]⁽*⁾⁽†⁾
          + ----------------------------------------------------------
     -prc = Number of parallel CPU processes to run.                   [Default: 8]                [-pc]
     -mem = Amount of memmory to be used (in GB).                      [Default: 16]               [-mm]
  -------------------------------------------------------------------------------------------------
  Total CPUs: 12 (max. MPI-procs.) :: System Memory: 5 GB
  -------------------------------------------------------------------------------------------------
  ⁽ᵃ⁾ From extracted tractory file (with TRAJS). [Complete procedure by default]
  ⁽ᵇ⁾ From extracted clusters file (with MICRO). [Partial procedure, without MICRO reexecution]
  ⁽*⁾ Each module can be run independently.
  ⁽†⁾ The “-key” option can be passed separately.

3.1.3. Quickstart Examples#

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