6.1. File menu

6.1.1. New Project

Create a new project.

The file structure of the created project is as follows.

Renaming of each file/folder is not supported. Since renaming of projects is not supported, it is recommended to leave a note in the Description of File ‣ Project ‣ Get Info about the role of the project, etc. Similarly for working folders, you can leave notes in the Description of File ‣ Project ‣ Selected Working Folder ‣ Get Info.

When moving project files, move the entire wmpjdata folder.

.wmpjdata folder: a folder containing all the files in the project. Drag and drop this folder into Winmostar to open the project.

.wmpj file: A file containing information about the project. Drag and drop this file into Winmostar to open the project.

temp.wmm : This file contains information on the molecular structure being edited.

index.ndx: the file where information on groups registered with select ‣ register group is stored.

.wmps* file: the workflow configuration file used for this project.

work* folder: working folder

Exec* folder: contains the files that control the jobs in each working folder.

6.1.2. New project with current structure

Create a new project using the structure currently displayed in the molecule display area.

6.1.3. Open Project

Open an existing project.

6.1.4. Open Recent Project

Open a recently opened project file.

6.1.4.1. Clear History

Empty the history of recently opened project files.

6.1.5. Project

6.1.5.1. Get Info

View information about the open project. Some information can be edited here.

6.1.5.2. Open Temporary File

Open a temporary file of the opened project.

6.1.5.3. Show in Explorer

Open the wmpjdata folder of the opened project.

6.1.5.4. Parameter/structure scan result display

You must purchase an add-on to use this feature. After a parameter scan or structural scan calculation, the results of each calculation can be tabulated.

Check All
Check all working folders in Working Folders.

Uncheck All
Uncheck all working folders in Working Folders.

Check Selected
Check the selected working folders in Working Folders; you can use Shift or Ctrl to select multiple working folders in Working Folders.

Working Folders
Check the working folder that contains the calculation results you want to visualize.

X Axis
Selects the value of the X axis for visualization.

X Axis
Selects the value of the Y axis for visualization.

Export csv
Outputs a csv file listing the physical properties for each working folder. When outputting a csv file from a graph, you can only select one physical property, but this function allows you to output multiple physical properties.

Export Animation
Create a wmm file with the values selected in End Structure and Property. For example, if you want to create a Volume-Total Energy graph, create an animation with this feature and then use the Custom Plot feature to select Volume for the X axis.

Draw
Create a graph with the conditions you set.

6.1.5.5. Selected Working Folder

Each function in this menu operates on the working folder selected with working folder in the project display area on the left of the main window.

The same menu is displayed by right-clicking on the working folder in the project display area.

6.1.5.5.1. Open Coordinate (Initial)

Displays the initial structure in the selected working folder. In most cases, this will be the input file for the job.

For the second and subsequent working folders in a series of generated working folders, the same initial structure as the first working folder will be displayed until the job is executed. After the job is executed, the original initial structure of the working folder is displayed.

6.1.5.5.2. Run

Runs the job in the selected working folder. Select Do not run jobs after saving files in the Job Settings window and use this function if you want to start the job later.

6.1.5.5.3. Stop

Stops (kills) jobs in the selected working folder.

6.1.5.5.4. Show Workflow Setup

Displays workflow settings for the selected work folder.

6.1.5.5.5. Show Keyword Setup

Displays keyword settings for the selected work folder. This corresponds to the contents of Details in the workflow settings.

6.1.5.5.6. Show Job Setting

Displays job settings for the selected working folder.

6.1.5.5.7. Control Remote Job/Server

Performs remote server operations for jobs in the selected working folder. Available only for remote jobs.

6.1.5.5.8. Show Command for Job Submission

Displays the command when a job in the selected working folder is submitted (SUBMIT) on a remote server. Available only for remote jobs.

6.1.5.5.9. Show Result of Job Submission

Displays the result of submitting (SUBMIT) a job in the selected working folder on a remote server. Available only for remote jobs.

6.1.5.5.10. Receive All Remote Output Files

Transfers all output files related to the job in the selected working folder from the remote server to the local machine. Available only for remote jobs.

6.1.5.5.11. Open Remote stdout

Opens the standard output on the remote server for the job in the selected working folder. Available only for remote jobs.

6.1.5.5.12. Open Remote stderr

Opens the standard error on the remote server regarding the job in the selected working folder. Available only for remote jobs.

6.1.5.5.13. Delete Remote Working Folder

Deletes the data in the selected working folder on the remote server. This operation cannot be reverted. It is available only for remote jobs.

6.1.5.5.14. Get Info

You can change the Description of the selected working folder; the Description will be the string set in the job description in the job settings window.

6.1.5.5.15. Recheck Status

Re-checks the status of the selected working folder. If for some reason the status is not determined correctly for a remote job (for example, ABORT is displayed even though the job has ended normally), this function will re-determine the status.

6.1.5.5.16. Delete

Deletes the selected working folder. This operation cannot be reverted.

6.1.5.5.17. Show in Explorer

The selected working folder is displayed in Explorer.

6.1.6. New File

Create a new file.

Hint

The shortcut is Ctrl+N .

6.1.7. Open File

Read the molecular structure from file into the main window. It corresponds to the format of various software.

Use Import File if you want to load the structure without switching the current mode file.

Hint

The shortcut is Ctrl+O .

6.1.8. Open Recent File

Open a recently opened file.

6.1.8.1. Clear History

Empty the history of recently opened files.

6.1.9. Reload

Re-load the file opened in the main window.

6.1.10. Save

Overwrites the currently open file or project.

For details, see Save As .

Hint

The shortcut is Ctrl+S .

6.1.11. Save As

Save the molecular structure displayed in the main window as a different name.

After saving, the saved file will be reopened. If you simply want to output the structure in the specified format without reopening it, use Export File.

It is recommended that you enter the file name and the folder name including all files (all upper layers) with one-byte alphanumeric characters only.

If multi-byte characters such as double-byte alphanumeric characters or Japanese characters or spaces are included, some processing may cause problems.

Underscores can be used.

When saving an input file of various solvers, a file is created based on the contents of Keyword Editor and Coordinate Viewer.

If the keyword of the solver you want to save is not displayed in Keyword Editor, Configuration window will open automatically. For MOPAC, GAMESS, Gaussian, NWChem, the coordinates are output in the format selected in File ‣ Coordinate Format.

Hint

The shortcut is Shift+Ctrl+S

6.1.12. Close

Closes the currently open project or file and returns to the startup screen.

6.1.13. Import File

Loads an existing molecular structure file. You can either discard the current structure and load it, or append it to the current structure and load it.

Open File opens the file in file mode when it is read in, but this function overwrites the structure of the molecular display area with the structure of the imported file without switching modes or files.

6.1.14. Import Recent File

Import recently used files.

6.1.15. Import

It reads a specific type of molecular structure.

6.1.15.1. SMILES

Molecular structure is generated from SMILES format string and read into the main window. When Import SMILES window opens, enter the SMILES format string in the text box and press Import button. Internally, conformational search by Bolloon or OpenBabel is also executed at the same time. A working folder named *_smiles_tmp will be created as an intermediate file.

6.1.15.2. Structural Formula

Create a molecule by entering a structural formula. Internally, JSME draws the structural formula, and Balloon or OpenBabel generates the 3D structure by generating SMILES from JSME.

6.1.15.3. Sample File

Load the files in the Samples folder.

6.1.16. Export File

Outputs the current molecular structure in any file format.

6.1.17. Export

Outputs the contents displayed in the main window in the selected format.

6.1.17.1. SMILES

Outputs the molecular structure displayed in the main window as a string in SMILES format. Not available when multiple molecules are displayed in the main window. Use OpenBabel on Cygwin. “Do you want to generate SMILES after completing the hydrogen atoms?” dialog, if “yes”, OpenBabel is executed via mol2 format with the -b option, if “no”, OpenBabel is executed via xyz format.

Warning

To use this function, CygwinWM setup is required.

6.1.17.2. Structural Formula

The image of the structural formula of the molecular structure displayed in the main window is output in SVG format. It can not be used when multiple molecules are displayed in the main window. I use OpenBabel on Cygwin.

Warning

To use this function, CygwinWM setup is required.

6.1.17.3. Image

Outputs the contents displayed in the main window in BMP or JPG format.

6.1.17.4. CHARMM crd File

Outputs the molecular structure displayed in the main window in CHARMM crd format.

6.1.17.5. SDF File

Outputs the molecular structure displayed in the main window in SDF format.

6.1.18. Get Info

Displays detailed information about the molecular structure displayed in the main window.

6.1.19. Open in Text Editor

Open the file displayed in the title of the main window with the text editor selected in the configuration window.

Note

After editing with the text editor, selecting Reload , you can reflect the change on the main window.

6.1.20. Show in Explorer

Open the directory one level higher than the file displayed in the title of the main window.

6.1.21. Exit

Quit Winmostar.