1.1. PACKS#
1.1.1. Simulation Box Creation#
The PACKS module mediates the creation of the simulation box, through the iterative use of the PackMol program. The module can be run from the main program or directly from the command:
packs ⟨input1.ext⟩ ⟨input2.ext⟩ {…} [⟨-options⟩]
where ext is one of the extensions recognized by Solvate Suite, inputN the files with the structures of the solute and solvent molecules, and “-options” a set of options for the configuration of the box to be created. The program accepts input and output file formats of Gaussian (com, gjf and log), ORCA (inp and out), xTB (xyz and xtb), GROMACS (gro) and PDB (pdb), common formats in Computational Chemistry.
Note
Simply type packs in the terminal and press enter to see the full list of execution options for the module.
The most common use of this module is to create an initial configuration for a system with a single solute molecule surrounded by a number of solvent molecules of a single type:
packs ⟨solute.ext⟩ ⟨solvent.ext⟩ -mol N
where N corresponds to the number of solvent molecules. In the case of ionic solutes, it is possible to include counter-ions with the command:
packs ⟨solute.ext⟩ ⟨solvent.ext⟩ -mol N -cnt couterion.ext
The program determines the number of counterions needed to neutralize the charge in the simulation box. In these cases, the number N of molecules includes the incorporated counterions. The Solvate program also makes it possible to create simulation boxes with solvent mixtures, in which case it is necessary to inform the proportion between the molecules:
packs ⟨solute.ext⟩ ⟨solvent1.ext⟩ ⟨solvent2.ext⟩ … -pro [N1:N2:N3…]
The initial box can also be created based on the molar concentration M of the solute (a situation in which there is more than one solute molecule in the box):
packs ⟨solute.ext⟩ ⟨solvent.ext⟩ -cco M
or based on molal concentration M:
packs ⟨solute.ext⟩ ⟨solvent.ext⟩ -bco M
The box density D is automatically adjusted based on the density of the solvent used (if it is part of the program’s database), or defined manually by the user:
packs ⟨solute.ext⟩ ⟨solvent.ext⟩ -mol N -den D
The list of parameterized solvents is obtained from the command:
packs -lst
Any of the parameterized solvents can be provided as input to the program in the simulation box creation step.
Several additional options for adjusting packaging parameters are available. The complete list can be accessed from the help menu of the PACKS module.
1.1.2. Execution Options#
packs ⟨solute⟩ {⟨solvent⟩} [⟨-options⟩]
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⟨solute⟩ = File with solute geometry (.com/log/inp/out/xyz/xtb/gro/pdb)
⟨solvent⟩ = File with solvent geometry (.com/log/inp/out/xyz/xtb/gro/pdb)
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-mol = Number of solvent molecules in the packing step. [Default: 0][=Determine] [-nm][Nmol]
-npk = Number of packing layers. [Default: 2] [-np][Npck]
-cel = Dimensions of the simulation cell (in nanometers). [Default: Not defined] [-dc][dCel]
-gap = Gap between solute and cell edges (in nanometers). [Default: Not defined] [-dg][gCel]
-bco = Molal concentration of the simulation cell (in mol·kg⁻¹). [Default: Not defined] [-bc][bCon]
-cco = Molar concentration of the simulation cell (in mol·L⁻¹). [Default: Not defined] [-cc][cCon]
-pro = Proportion between solvent molecules. [N1:N2:...] [Default: Not defined] [-pr][Prop]
-den = Density of the simulation cell (in g·mL⁻¹). [Default: 1.0] [-ds][Dens]⁽*⁾
-cnt = File with counterion to be added for charge neutrality. [Default: None] [-ci][cIon]
-shp = Packaging format (sphere|cube|box). [Default: Sphere/Cube] [-sp][Shape]
-fmt = Type of generated file (inp|gro). [Default: Auto] [-ft][Format]
-tol = Minimum distance tolerated in packing (in Å). [Default: Not defined] [-to][Tolera]
-rep : Resubmit the packing procedure with new parameters. [Default: No] [-rp][Repack]
-for : Run in forced mode (no warning messages). [Default: No] [-fm][Force]
-nor : Run in normal mode (conventional packing configuration). [Default: No] [-cv][Normal]
-ite : Run in iterative mode (to adjust tolerance). [Default: No] [-it][Iterat]
-inc : Insert external force field into generated topologie. [Default: No] [-in][Include]⁽†⁾
-fft = Force field parameters. [OPL|GRO|CHM|AMB|LPG|QFC|ATB] [Default: OPLS/AA] [-ff][FField] ⁽†⁾
-bak : Save original input files. [Default: No] [-bk][Backup]
-svt = Solvent to be used in C-PCM/ALPB solvation model. [Default: Auto] [-sv][Solvent]
-lst : Lists the set of solvents in the database. [Default: No] [-ls][List]
-chk : Checks the consistency of simulation box settings. [Default: No] [-ck][Check]
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⁽*⁾ Configurable options in automated mode. ⁽†⁾ GROMACS only