11. Known problems

11.1. 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)

11.2. Some software does not work if you enable the Windows “Use Unicode UTF - 8 for worldwide language support” option.

In English version Windows 10 (1803), if the check box is checked in [Control Panel] - [Region] - [Administrative] - [Change system locate …] - [Use Unicode UTF - 8 for worldwide language support] There was a report that FDMNES execution failed. This is a problem caused by fdmfile.txt being read at FDMNES execution being output with BOM. Winmostar is sequentially corresponded at the timing of the problem, but please contact us if similar problems occur with other functions. (Reported on May 25, 2018)

11.3. 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)

11.4. The graph display at the bottom of the Animation window collapses. Other UI display collapses.

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)

11.5. 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)

11.6. 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)

11.7. Gromacs Chi or DPD parameter calculation function outputs 0.5 times the original definition.

If you are a V9 or V8 user, please update to 9.0.2 or later or 8.027 or later where the bug has been fixed. Since V7 is outside the support period, please be careful about the calculated value. (Reported on June 2, 2019)

11.8. 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)

11.9. When outputting an animated GIF from the animation window, an error may occur if the number of frames is large.

Use Export JPEG Images to output serial JPEG files, and then create animation files using various movie creation software. (Reported on January 29, 2020)

11.10. 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)

11.11. 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)

11.12. 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 April 20, 2021)

11.13. 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)

Hint

**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.**

11.14. An Access Violation error occurs when trying to output an animated GIF from the Animation window.

This may occur when the number of frames is large or when the number of atoms is large. In the Animation window, click [File]-[Export JPEG Images…]. in the Animation window, and then convert the sequential JPEG file to an animation file using any video creation software. In the future, we plan to radically improve the animation output function to solve this problem. (Reported on February 17, 2022)