6.21. Tools ‣ Preferences menu

We make various settings of Winmostar.

Basic Tab

Language

Select a language.

License code

Set the license code.

Internal UNIX environment

Choose whether to use cygwin for internal UNIX environment or Windows Subsystem for Linux (Bash on Ubuntu on Windows).

Use internal editor at [File]-[Open in Text Editor]

If checked, use Edit-> Direct Editor function up to V8 when you click File ‣ Open in Text Editor. If not, use the program set in Editor with Preferences ‣ Program Path.

Use old function adopted up to V8 for unzip

In the remote job, specify the code used to get and unzip the zip file of the working folder from the remote server. Old-style code generates errors when decompressing huge files (hundreds of MB or more).

Use old format adopted up to V9 when saving xyz file

When saving in xyz file format, save as xyz file without header which was the default before V9.

Output cell shape to save Xyz file

Output cell shape when saving in xyz file format.

Automatically adjust bond length and hydrogen after reading ChemDraw MOL format.

Automatically adjusts the bond length and hydrogen after reading the MOL format of ChemDraw.

Output residue number to save Xyz file

Output the residue number at the end of each line when saving in xyz file format.

Maintain project display area when opening files

Specifies whether the project display area is automatically hidden or maintained when switching to file mode.

Number of recently used files/projects

Specify the number of recently used files/projects.

Use external viewer to display Cube files

Use an external viewer (such as VESTA) instead of Winmostar Viewer to open Cube files. The program selected in the Cube Viewer in the program path will be used.

CIF file parse

Specifies the library to use for reading CIF files. Gemmi is the method implemented since V11.6.0. pymatgen was the method used prior to V11.5.X.

Use legacy filename for [Tools]-[Radius of Gyration]

Toggle the name of the output file between V11.6.0 or earlier format or V11.6.1 or later format in [Tools]-[Radius of Gyration].

Edit tab

Bonding Factor

Set the threshold for judging the presence or absence of covalent bond from interatomic distance.

Keep Z-Matrix connectivity while modifying structure

If checked, make sure that the Z-Matrix join relationship does not change when editing molecular structure.

Convert aromatic ring to single + double bond for MOL file

When storing the MOL file, change the aromatic ring to a combination of single bond and double bond before outputting.

Bonding exceptions

Use this function when you do not want to create bonds between specific elements in the function to automatically generate bonds. First press the Add button. Then select the two elements you want to exclude the join in the two pull-down menus below the list and press the Apply button. After that, applying Regenerate All Bonds etc will break the bond between the specified elements. To restore, select the line you want to unset from the list andpress the Delete button.

Move markers to pasted atoms.

If checked, move the marker to the pasted atom when using Paste.

Simple Structural Optimization Methods

Choose the method you want to use with Quick Optimization.

Force field, cutoff, threshold (OpenBabel)

Specify the parameters when the simple structural optimization method is OpenBabel.

Max # of atoms to show atom list

Set the maximum number of atoms to display coordinates in Coordinate Viewer.

Max # of atoms to show atom list

Set the maximum number of atoms to display coordinates in Coordinate Viewer.

Max # of atoms to generate Z-Matrix

Set the maximum number of atoms to automatically generate Z-Matrix.

Max # of atoms to generate bonds

Set the maximum number of atoms to automatically generate Z-Matrix.

Show [CH3], [C2H3] and [C6H5] buttons

Install a fragment selection shortcut button on the toolbar. (similar to V10 and earlier)

Show toolbar captions

Show captions such as “solver”, “element”, “fragment”, etc. in the toolbar.

When right-clicked on viewport

Show context menu

Displays a context menu when right-clicking in the molecule display area.

Replace with fragment

Replace with fragment when right-clicking in molecular display area. (as before V10).

Alphabetically sort fragment list

Sort the list of fragments alphabetically. (as before V10).

Calculation tab

General

Run MOPAC using Job Manager

When checked, use Winmostar Job Manager when executing MOPAC. If it is not entered, Winmostar will be in a wait state until calculation by MOPAC is completed, and the output result of MOPAC will be automatically loaded into the main window.

It can also be set from Use Job Manager.

Run the other solvers using Job Manager

Specify whether to use Winmostar Job Manager to execute programs other than MOPAC.

max # of Jobs

Sets the maximum number of jobs for the Job Manager.

Timeout

Set the time-out period of time-consuming processing.

Use old format adopted up to V9 when saving xyz file

If checked, use the directory name with “wm_” appended to the user name for the work folder Remote Job Submission.

QM

Forcibly sleep after GAMESS run

If this is checked, GAMESS will be forced to sleep for the specified number of seconds after executing GAMESS on the local machine. This function is useful when you want to check the contents of a log immediately after calculation.

mpiexec (NWChem)

Specifies the mpiexec to use for parallel computation in NWChem local jobs. For MPICH, the mpiexec specified in the program path is used. For Select, any mpiexec can be specified.

Options for mpiexec (NWChem)

mpiexec (NWChem) where Select is the argument for the mpiexec command. Where %WM_NUM_PROC% is entered, the parallel number is automatically assigned at runtime. (For example, if you enter -np %WM_NUM_PROC% in Options for mpiexec (NWChem) to calculate 2 parallelisms, mpiexec will actually run with the argument -np 2. )

# of procs for RESP charge calculation (GAMESS)

Specify the number of parallels for automatic calculation of RESP charges using GAMESS.

Keywords for automatic RESP charge calculation (GAMESS)

Sets the keyword for automatic calculation of RESP charges using GAMESS. By default, the keyword to perform a single point calculation with HF/6-31G* is used.

MD

Modify charges from AmberTools to adjust total charge

When calculating AM1/BCC, Gasteiger, and RESP charges using acpype or AmberTools, the charge of the entire molecule is set to a strictly integer value. In this case, the value of the charge of the first atom in the molecule is slightly modified.

Retain residue and atom names during force field assignment

Sets whether residue and atom names are retained during force field assignment.

mpiexec (LAMMPS)

Specifies the mpiexec to use for parallel computation in LAMMPS local jobs. For MPICH, the mpiexec specified in the program path is used. For Select, any mpiexec can be specified.

Options for mpiexec (LAMMPS)

mpiexec (LAMMPS) where Select is the argument for the mpiexec command. Where %WM_NUM_PROC% is entered, the parallel number is automatically assigned at runtime. (For example, if you enter -np %WM_NUM_PROC% in Options for mpiexec (LAMMPS) to calculate 2 parallelisms, mpiexec will actually run with the argument -np 2. )

Using double precision in MD results analysis

Sets whether gmx (single precision) or gmx_d (double precision) should be used for result analysis with Gromacs.

Update elements when top file is loaded

When reading a top file in Gromacs force field assignment, set whether elements are read from the top file and reflected in the model.

Version of LAMMPS to be used

Specifies the version of LAMMPS to which the output LAMMPS input file corresponds. The output format of some keywords (e.g. thermo_style) will vary depending on the version.

LAMMPS Potential Folder

Set about the LAMMPS potential folder.

Open potential directory

Open LAMMPS potential folder in Explorer.

Consolidating the same parameter type in LAMMPS data files

Sets whether the same parameters Bond type, Angle type, Dihedral type, and Improper type are merged in the output LAMMPS data file.

Allow LAMMPS pair_style, Potential file input

In the force field assignment function, allow users to freely input pair_style and Potential file.

Solid

Distance tolerance for Spglib

Sets the tolerance for automatic crystal symmetry detection in Spglib

Warn calling Spglib if # atoms is more than

Sets the minimum number of atoms to skip Spglib execution.

Default extensions

Set the extension set by default when creating input files for each solver.

Open k-path file

Open a file that sets the default k-point path for calculating band structure in Quantum ESPRESSO and OpenMX. Set per ibrav in Quantum ESPRESSO.

mpiexec (QE)

Specifies the mpiexec to use for parallel computation in Quantum ESPRESSO local jobs. For MPICH, the mpiexec specified in the program path for MPICH2 is used. For Select, any mpiexec can be specified.

Options for mpiexec (QE)

mpiexec (QE) where Select is the argument for the mpiexec command. Where %WM_NUM_PROC% is entered, the parallel number is automatically assigned at runtime. (For example, if you enter -np %WM_NUM_PROC% in Options for mpiexec (QE) to calculate 2 parallelisms, mpiexec will actually run with the argument -np 2. )

Version of QE to be used

Specifies the version of the QE to which the input file of the output QE corresponds. The output format of some keywords (&fcp, HUBBARD, etc.) is diffrent with the version

QE pseudo directory

Setup about pseudopotential folders for Quantum ESPRESSO.

Open QE pseudo directory

Open Quantum ESPRESSO pseudopotential folder in Explorer.

Download pseudo files

Automatically download pseudopotential files from the web server to the Quantum ESPRESSO pseudopotential folder.

Open priority list

Sets the order of the list of Pseudo potential choices in the Quantum ESPRESSO Keyword Settings window. Asterisks can be used as wildcards.

QE MOL directory

Specify a folder to contain the solvent files for the RISM-compatible version of Quantum ESPRESSO.

View Tab

Color set

Select the color set from Winmostar, GaussView, Jmol, Rasmol, and Old Winmostar.

Color

Selected atom

Change the color of the atom type of the selected particle.

Bond

Change the color of the bond.

Background

Change the color of the background.

Background (Viewer)

Change the background color of Winmostar Viewer.

Text

Change the color of the character on the molecule display window.

Color bonds with color of atoms

Colors the bonds with the color of the atoms.

VDW radius of selected atom

Change the VDW radius for the element of the atom with marker in Viewport.

Diameter of bond

Specifies the diameter of the bond.

Font size on Keyword Editor

Specify the font size of the Keyword Editor.

Scrolling speed

Adjust the speed of zoom in/out by the mouse wheel in Viewport.

‘Min # of atoms to switch to wire model while zooming’

Sets the minimum number of atoms to be changed to the wire model during zooming.

‘Time to return from wire model after zooming [msec]’

Sets the time in milliseconds to return from the wire model after zooming.

Depth cue

Adjusts the fog density used for depth expression.

Depth cue density

Adjusts the fog density used for depth expression.

Maximum # of atoms for depth cue

Enable depth cue if the number of atoms is greater than the specified value.

View center after opening file

Check View Marked Atom autoatically when opening a file.

‘Interval to show hint [msec]’

Set the wait time in milliseconds for hints to appear when hovering the mouse cursor over various controls.

‘Font size for hint’

Sets the font size of the hints that appear when the mouse cursor hovers over various controls.

Items to be drawn

Check the items to be displayed in Viewport.

You can also be set from View ‣ Items.

Scaling factor of charge

Adjust the size of the charge display when displaying charges in Label/Charge.

You can also be set from View ‣ Items.

Program Path Tab

Specify the install path of various programs.

For MOPAC and GAMESS, multiple program paths can be specified. In project mode only (1) is used. In file mode, you can use QM ‣ MOPAC and QM ‣ GAMESS in the run menu. The program invoked by the Run button in the file mode keyword setup window is the program path set in (1).

For Quantum ESPRESSO, select pw.exe out of several executables.

%APPDIR% is an alias character indicating the Winmostar installation folder and %CYGWINDIR% is the CygwinWM installation folder.