12. Known problems

12.1. If you start Winmostar with administrator privileges, you can not open files with drag-and-drop.

In the current Winmostar (Winmostar V.8), if you start Winmostar with administrator privileges, you can not open the file by dragging and dropping. It is due to be fixed in the future, but the working time is unknown. (Reported on May 24, 2018)

12.2. Some software will not work if the Windows option “Use Unicode UTF-8 for worldwide language support” is enabled.

In Windows 10, if [Control Panel] - [Clock and Region] - [Change Date, Time, and Numeric Format] - [Manage] - [Change System Locale] - [Use Unicode UTF-8 for World Wide Language Support] is checked, various remote job executions, LAMMPS execution, and FDMNES execution failed when the “Use Unicode UTF-8 for World Wide Language Support” checkbox is checked. The problem is due to files being output with a BOM. We are working to address Winmostar sequentially at the time the problem occurred, but please let us know if you experience similar problems with other functions. (Reported May 25, 2018)

12.3. Opening some subwindows such as Animation, Submit Job and so on, it will not appear even if you try to open again after closing.

It has been confirmed in only a few environments. If it does not appear, a menu such as [Return to original size] [Move] [Size change] … will appear when you press Alt + Space key, so when selecting [Move] and dragging it, the window reappears I will. Alternatively, it can be resolved by restarting Winmostar. We are currently considering better countermeasures. (Reported on 14th June 2018)

12.4. Graph display at the bottom of animation operation area is corrupted. Other UI displays are corrupted.

If you change the size of desktop text or other items from the default value (100%), the display will collapse. For Windows 8, set [Control Panel] - [Customize Desktop] - [Display] - [Change the size of all items] to Small -100% (prescribed). For Windows 10, set [Windows setting] - [system] - [display] - [custom scaling] to [100]. (Reported on June 26, 2018)

12.5. If you select a range of text in the console window where the job of the local machine is flowing, the job is recognized as terminating on Job Manager.

In the Windows 10 console window, selecting the range of the log text of the job being executed will recognize that the job has ended. If this causes a problem, open the log file to be output directly with a text editor, and select and copy the range of the text there. If processing is interrupted after selecting the range, processing will resume by pressing the Enter key. It occurs in Windows 10 or later. (Reported on July 20, 2018)

12.6. Gromacs freezes while running Gromacs on local machine.

On some machines, Gromacs freezes while running Gromacs on the local machine. It occurs during MD calculation and the contents of standard output do not change. There is no reproducibility in the place where it freezes. In such cases, you can avoid by setting “# of Threads” of Gromacs Configure to 1. As a matter of course, processing becomes slower, please use remote job submission function using remote server if you want to run full-scale calculation. LAMMPS can be used with Winmostar in a similar way to Gromacs, so you can also choose to use LAMMPS. (Reported on December 4, 2020)

12.7. When using the RISM compatible version of Quantum ESPRESSO, it may be displayed that the main window keyword has been changed even though it has not been changed.

During constant-mu calculation (lfcpopt = .True.), it is erroneously determined that the value of fcp_mu has been updated. Since the value is not actually changed, it can be used as is. (Reported on June 2, 2019)

12.8. The units of Isothermal Compressibility and Adiabatic Bulk Modulus output by Gromacs are wrong.

In the gmx energy log, the units for Isothermal Compressibility is “J/m^3”, but the correct unit is “m^3/J”. Similarly, the Adiabatic Bulk Modulus unit is correctly “J/m^3”. (Reported on June 29, 2020)

12.9. Molecules that should be connected to each other are displayed separately in the structure or the final structure after loading the Gromacs trajectory.

This is due to a bug in Gromacs itself. The longer the calculation time, the more likely it is to occur. However, there is no problem with the MD calculation itself, since the atomic configuration is correct when periodic boundaries are taken into account. The problem occurs especially when two systems are joined by an interface builder. There are two ways to put a disjointed molecule back together. The first method is to select [MD]-[Gromacs]-[Assign Force Field], then [Use Parameters Written in Topology File] and select the top file of the target data. In the second method, first, in [Edit]-[Rearrange atoms based on periodic boundary conditions], click [Rearrange atoms inside cells atom by atom] → click [Apply] → click [Revert rearranged structure atom by atom] → click [Apply] → click [OK]. However, since this operation must be performed in the same cell as when the calculation was performed, please perform it before using the interface builder, etc. (Reported on December 25, 2020)

12.10. When loading SMILES strings using [File]-[Import]-[SMILES], but the structure is not loaded as intended.

There are several programs in the world that load SMILES, and each of them has a slightly different implementation that can change the molecules generated. Winmostar uses either OpenBabel or Balloon to import SMILES, and you can choose which one to use in the Import SMILES window.

For example, in OpenBabel, “C[C@@H]1CCCC[C@@@H]1C” (originally cis-1,2-Dimethylcyclohexane) was recognized as trans-1,2-Dimethylcyclohexane. (Reported on January 29, 2020)

12.11. Winmostar freezes when deleting the working directory or working folder directly on Windows (Explorer) while Winmostar is processing.

Delete when the process is finished or when Winmostar is closed. (Reported on December 24, 2021)


**working folder**

  • A working folder is a folder whose name is the name of the file opened in the main window plus a suffix.

    • **The suffix varies depending on the type of solver.**

    • For example, in Gromacs, if the file opened in the main window is aaa.gro and the suffix is _gmx_tmp, the working folder will be named aaa_gmx_tmp.

  • It must be placed in the same directory as the file opened in the main window.

  • The process runs in a working folder of the same name during a continuation job, but by default, a backup of the working folder of the previous job is created just before the continuation job is executed.

    • The name of the backup will be the one with the lowest number, as long as there are no duplicate names. For example, if your working folder is aaa_gmx_tmp, then it will be aaa_gmx_tmp1.

    • **Un-numbered directories are always up-to-date.**

12.12. Cannot open large size cube file in Winmostar Viewer.

Please use other cube file visualization software such as VESTA or VMD. You can directly launch them instead of Winmostar Viewer by checking [Tools]-[Preferences]-[Basic]-[Use external viewer to display cube files] in Winmostar and specifying the cube file visualization software in [Program path]-[Cube Viewer]. You can directly start those software instead of Winmostar Viewer. (Reported October 21, 2022).

12.13. Winmostar toolbar and tool buttons are displayed incorrectly when Windows display magnification is other than 100%.

In Windows 10, this can be changed by going to Settings→System→Display→Scaling and Layout. If the display is too small to read the text, reduce the screen resolution. (Note that this feature in Windows is also a problem for various applications other than Winmostar.) (Reported on October 28, 2022)

12.14. Under some conditions, LAMMPS fails to recognize elements in the structure file after the calculation is completed when using a potential file.

For example, if you use the MEAM potential available in the NIST repository to calculate the mass of a Sn crystal, the file output by the write_restart command will show a mass of “118” instead of “118.7107”. Winmostar recognizes elements based on their mass values, and if it cannot recognize an element, it judges it as a coarse-grained atom such as CGA. This is a bug in LAMMPS (at least confirmed in the 20160309 version), so please correct the masses in the Masses section of the final structure data file using a text editor, etc. (Reported on December 8, 2022)

12.15. Cannot exit a job from the Stop menu from Job Manager in Windows 11.

Please close the calculation window or terminate the process using Task Manager or similar. In the case of NWChem, some users have reported that the CPU usage of the Job Manager becomes so high that it cannot even be terminated. (Reported on May 20, 2023)