11.1. How to launch from the command prompt
Recognize input files as SMILES and build molecules
(using Balloon)
(Professional Edition Premium Elite Only)
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smilesballoon |
Recognize input files as SMILES and build molecules
(using OpenBabel)
(Professional Edition Premium Elite Only)
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smilesbabel |
Execution of MOPAC |
-mopac1, -mopac2, -mopac3
These correspond to the three MOPAC binaries selected in Tools ‣ Preferences menu .
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-molsv |
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-aspect |
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-radgyr |
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-adjust |
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-hadd |
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-hdel |
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-clean |
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Use RESP charges (only for one molecule) |
-resp (charge value, 0 for neutral molecules) |
Use AM1-BCC/Gasteiger charges (only for AM1-BCC one molecule)
(Professional Edition Premium Elite Only)
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-am1bcc (charge value, 0 for neutral molecules) (Professional Edition Premium Only) |
Solvate/Build Cell (the first argument is ignored) |
-pack (file name of 1st molecule type):(number of 1st molecule type):(file name of 2nd molecule type):(number of 2nd molecule type) … (density [g/cm^3]) |
Insert Molecules
(Professional Edition Elite Only)
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-insertmol (file name of 1st molecule type):(number of 1st molecule type):(file name of 2nd molecule type):(number of 2nd molecule type) … (enumerated similarly thereafter) |
Calculation of LAMMPS (Local Job)
(The lmpset file can be obtained from the Save button in the LAMMPS Preference window.)
(lmpset files are specified by relative path from the first argument)
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-lammps (type of forcefield) (preset name or lmpset file name of the 1st job):(preset name or setting file name of the 2nd job) … (parralel number)
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Output LAMMPS coordinate file
(see Assign Force Field for force field type)
(Professional Edition Premium Elite Only)
Specify UFF or Dreiding as “GAFF(1=UFF)” etc. for a partial species in the force field for general molecules.
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-lammpsfile (type of force field for general molecules) (type of force field for water molecules) (name of data file to output) |
Output Gromacs coordinate and force field files
(see Asign Force Field for force field types)
(Professional Edition Premium Elite Only)
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-gromacsfile (type of force field for general molecules) (type of force field for water molecules) (name of output gro file) (name of output top file) |
-slabbuilder (h) (k) (l) (supercell size in direction a) (supercell size in direction b) (true if cells are forced to be rectangular, false otherwise) (true if slab size is specified per unit cell, false if specified in angstrom) (slab size value) (vacuum layer size value) (true if surface is hydrogen terminated, false otherwise) (true if vacuum layer is not inserted) |
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-slab (h) (k) (l) (supercell size in direction a) (supercell size in direction b) (true if you want to force the c axis to be perpendicular to the a and b axis, false otherwise) (true if you want to convert hexagonal to orthorombic, false otherwise false) (true if you want to specify the minimum slab size as number of hkl planes, false if you want to specify it as angstrom) (minimum slab size value) (c-axis length of the entire system) |
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(Professional Edition Elite Only)
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-supercell (number of cells along axis a) (number of cells along axis b) (number of cells along axis c) (regenbond to regenerate bonds, noregenbond not to regenerate bonds) |
Deform cells in uniaxial direction
(Professional Edition Elite Only)
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-editcellaxis (inclen to specify the change in cell size, totlen to specify the cell size after the change, strain to specify the strain, density to specify the density after the change) (value to specify) (axis direction (a, b or c) to deform) (posi for + direction, nega for - direction, both for the both direction) (keepfrac to keep the fractional coordinates, nochange to keep the fractional coordinates) (keepintra to keep the coordinates in the numerator, nokeep to keep the coordinates in the numerator) |
Change file type and save |
-o output_file_extension |
Save the file by specifying a file name
(if a relative path is specified, the UserData folder is the starting point)
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-outfile output_file_name |
- Use case:
\"C:\\winmos11\\winmostar.exe\" COO -s -smilesballoon -outfile ethanol.mol2 \"C:\\winmos11\\winmostar.exe\" \"C:\\winmos11\\samples\\dbt.dat\" -s -mopac1 \"C:\\winmos11\\winmostar.exe\" \"C:\\winmos11\\samples\\dbt.dat\" -s -molsv 1 2.0 0.02 \"C:\\winmos11\\winmostar.exe\" \"C:\\winmos11\\samples\\dbt.dat\" -s -o pdb \"C:\\winmos11\\winmostar.exe\" \"C:\\winmos11\\samples\\dbt.dat\" -s -adjust -hadd -clean -o gjf \"C:\\winmos11\\winmostar.exe\" \"C:\\winmos11\\samples\\ch4.mol2\" -s -pack ch4.mol2:100:ethanol_am1.mol2:2 0.6 -outfile ch4_100_etoh_2.mol2 \"C:\\winmos11\\winmostar.exe\" \"C:\\winmos11\\samples\\ch4_100_etoh_2.mol2\" -s -lammps "Dreiding" "Minimize (fast):NVT (fast):NPT (fast)" 2 \"C:\\winmos11\\winmostar.exe\" \"C:\\winmos11\\samples\\ch4_100_etoh_2.mol2\" -s -lammpsfile GAFF SPC/E ch4_100_ethoh_2_auto.data