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, the more likely it is to occur. However, there is no problem in the MD calculation itself, because the atomic configuration is correct when the periodic boundary is taken into account. The problem occurs especially when two systems are joined by an interface builder. If you want to restore the disassembled molecules, click [Edit]-[Wrap Around Cell Boundary], click [Wrap for each atom], click [Apply], click [Unwrap all molecules], click [Apply], and then click [OK]. However, since this operation must be performed in the same cell as when the calculation was made, please perform it before using the interface builder. (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)