10.1. How to launch from the command prompt

It is possible to start by specifying various options from the command prompt.
Specify the input file name and processing contents in the option.
The processing contents that can be specified are as follows.
Recognize input files as SMILES and build molecules
(using Balloon)
(Professional Edition Premium Only)

smilesballoon

Recognize input files as SMILES and build molecules
(using OpenBabel)
(Professional Edition Premium Only)

smilesbabel

Execution of MOPAC

-mopac1, -mopac2, -mopac3
These correspond to the three MOPAC binaries selected in Tools ‣ Preferences menu ‣ Program Path.

Molecular Surface Area & Volume

-molsv

Aspect Ratio

-aspect

Adjust All Bond Lengths

-adjust

To all atoms

-hadd

Delete All Hydrogens

-hdel

Quick Optimization

-clean

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 Only)

-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])

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)
-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)
Output LAMMPS coordinate file
(see Assign Force Field for force field type)
(Professional Edition Premium Only)

-lammpsfile (type of force field for general molecules) (type of force field for water molecules) (number of parallels) (name of data file to output)

Output Gromacs coordinate and force field files
(see Asign Force Field for force field types)
(Professional Edition Premium Only)

-gromacsfile (type of force field for general molecules) (type of force field for water molecules) (number of parallels) (name of gro file to output) (name of top file to output)

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)

-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
Specify input file at first argument.
When -s is specified, Winmostar ends automatically after processing, so you can write DOS BAT file and run MOPAC etc. continuously. See Sampleswmjobs.bat for reference.
Commands starting with “-” except “-s” are executed in the order specified.
If you want to run Gaussian and GAMESS sequentially, use Tools ‣ Batch Queue instead.