12. Frequently asked questions · Troubleshooting
Q. Process using Cygwin will end abnormally. / function will display … ERROR …. / Cygwin’s black window shows child_info_fork :: abort: … Loaded to different address: parent …! = Child ….
Q. function displays No reference file (… filelist_cygwinwm.txt) was found….
Q. function will display WARNING … some files are missing.
Q. In the functions where a black console window appears, such as various functions of Winmostar or the execution of the solver, the processing of the black console window does not end and does not proceed.
Q. function will display Error: Failed to solvate. and processing will fail.
The Hamiltonian calculation method (Hamiltonian) or basis function (Basis Set) that I want to use is not found in the Configure window or the Easy Setup window for MOPAC, GAMESS, Gaussian and NWChem. How do I set it up?
Q. Immediately after installing GAMESS for Windows, I was able to use it without any problems, but at some point, all the calculations started to terminate abnormally in the middle. Is there a way to fix this?
Q. When I load the final structure or animation from Gromacs, or when I edit it in some way and then run the MD calculation again, the force field assignment fails or the MD calculation breaks down. Is there a solution?
Q. When calculating the dielectric function using Quantum ESPRESSO, “USPP are not implemented” is displayed in the epsilon.x output (eps.out) and it is not possible to acquire the dielectric function.
Q. Quantum ESPRESSO terminates normally for systems with a small number of atoms, but for large systems it terminates abnormally with an error such as “cannot allocate …”. for large systems. What can I do about this?
Q. When calculating the Hansen solubility parameter of a polymer using the solubility parameter calculation module, the output value changes depending on how the repeating structure (monomer) of the polymer is taken.
12.1.4. Q. Is it possible to split the price of Winmostar and maintenance? Is it possible to sell maintenance only?
12.1.7. Q. I am both an educational and research institution. Can I use my institution’s budget to purchase a license for an educational institution?
This is not possible in the case of private companies and public offices. For educational institutions, it is possible to change if more than one year has passed since the last user change (or purchase if it is the first time).
12.2.2. Q. If I move from the institution where I purchased my educational license to another institution, can I continue to use that license?
If you are no longer affiliated with the institution at the time of purchase, you will not be able to use the software, even if it is a perpetual license. This is because the license for educational institutions is specially priced for students, researchers, and faculty who belong to the educational institution and use the software only for the educational institution’s business.
12.2.3. Q. Do I need to reinstall the software when I change editions, such as from a free edition to a student edition, or from a free trial to a professional edition?
12.2.4. Q. Can I install different editions of Winmostar, such as the free version and the professional version?
Winmostar V10 or lower and Windows 10, first clickto launch the command prompt. Next, in the Command Prompt window, type ipconfig /all and press Enter. Various information will be output, look for the “physical address” line in the output. Its contents are the MAC address.
If there is more than one “physical address” line, basically any “physical address” can be used as the MAC address for Winmostar’s node-locked license purchase.
12.2.7. Q. Does Winmostar license fee include Gaussian license fee, and is there a Winmostar lineup with Gaussian license?
12.2.9. Q. Can I purchase a license for an educational institution for my personal learning purposes?
X-Ability Co. Ltd.. Place of manufacture is Japan.
12.4.4. Q. Is it possible to use the data generated by Winmostar for conference presentations and papers? How should I quote at conference presentations and paper submissions?
12.4.5. Q. Is it possible to upload videos or images of the Winmostar screen to YouTube or other web sites?
12.4.11. Q. Is there an upper limit to the number of cores that can be used for parallel computing using Winmostar? Does the cost vary depending on the number of cores available?
For instructions on installing Gaussian, get them from your Gaussian distributor. After installing Gaussian, In the, select the Gaussian program path(g03.exe, g09.exe, g16.exe etc.).
12.4.14. Q. How many atoms or molecules can I calculate with Winmostar? Is there an upper limit to the number of atoms or molecules that can be handled?
Assuming that the operating speed is not considered, we have confirmed the operation of up to about 1 million atoms. Since the operating speed strongly depends on the execution environment, please check it with the free trial before purchasing. We are planning to increase the speed of Winmostar in future versions.
As coarse-grained models in the sense that they are not pure quantum chemical, ab initio, or classical molecular dynamics calculations, dissipative particle dynamics (DPD) calculations using LAMMPS and the Kremer-Greset model are supported (please inquire separately for Kremer-Greset). The United atom model and its derived coarse-grained models will be supported in the future. For other models, please contact us separately. The reason for this is that we recognize that most research using coarse-grained models cannot be meaningfully accomplished by simply using the software, but requires careful consulting. Winmostar’s support case study shows the simulation results of a well validated coarse-grained model.
First, please perform the following basic checks.
Check the Installation precautions.
Check whether Winmostar in use is a free version, a student version, a professional version, or a professional version (trial), and whether the function causing the problem is available in that version with function table.
Check the activity record of the security software in use and check whether there is any record in which the activities of the application under Winmostar and CygwinWM installation folder are disturbed.
Update Winmostar to the latest version (it is possible to coexist with the version you are using), check if there is a situation similar to Known problems and Frequently asked questions · Troubleshooting.
If the names of files to be saved and directories containing them (including all upper layers) contain multibyte characters such as Japanese and special symbols including sapces, some solvers may cause problems. Therefore, use only single-byte alphanumeric characters.
Check the working folder to see if the log is being output by the executed process and check the contents of the log.
If calculation is started but the calculation result is wrong, click “Open Log File” etc from the solver menu used in the main menu and check the contents of the log.
For the calculation failure, check that the version of the solver is the same as the version recommended in the Winmostar installation guide. (Especially Gromacs, LAMMPS, or Quantum ESPRESSO)
Trace again to confirm that it is not a misoperation.
If parallel execution is performed, switch to serial execution (parallel number 1).
Restart the OS.
With security software, Exclude Winmostar, installation folder of CygwinWM, and solvers including MPI from monitoring.
If you are using CygwinWM, runand perform a simple diagnosis of CygwinWM.
Reinstall Winmostar, CygwinWM and the solver you are using.
Try with another PC.
Next, trace the tutorial which seems to be as close as possible to what you want to calculate finally. If it succeeds, please change the calculation condition such as Number of atoms, size of super cell, degree of polymerization, type of element, number of phases, etc. so that it finally gets to calculate what you want to calculate and try to identify where the problem occurs.
12.5.3. Q. Process using Cygwin will end abnormally. / function will display … ERROR …. / Cygwin’s black window shows child_info_fork :: abort: … Loaded to different address: parent …! = Child ….
A. Please do the following procedure one by one from the top, and re-do the process where the error occurred each time.
Perform general dealing with common problems.
Restart your PC
Open Windows Security and go to App & browser control and click Exploit protection. Then change the value of Force randomization for images to Off by default or Use default (Off).
Search and delete anything other than
cygwin1.dlland restart the machine
This operation is necessary in some cases if
cygwin1.dllexists in addition to CygwinWM on the same machine.
cygwin1.dllmay be included in various freeware etc even if you do not install Cygwin in other location.
With all Cygwins on the machine being used terminated, at the [Run] of Windows
C:\cygwin_wm\bin\ash.exe(when CygwinWM is installed in
C:\cygwin_wm), execute the /bin/rebaseall -v, and restart the machine.
Temporarily disable security software.
Disable software that tends to cause problems described in Cygwin FAQ .
In addition, try the method described in Cygwin FAQ fork() related failures.
Install a new version of Cygwin from the Cygwin official site and check if you can start a terminal.
C:\cygwin_wm) and specify the folder directly above it in [Tools]-[Preferences]-[Program Path]. Find filelist_cygwinwm.txt in the location where CygwinWM was installed (by default
C:\cygwin_wm) and specify the folder directly above it in [Tools]-[Preferences]-[Program Path]. If you cannot find filelist_cygwinwm.txt, the installation of CygwinWM may have failed, so please review the settings of your security software and reinstall CygwinWM.
12.5.7. Q. When executing a job, an alert saying “Unable to execute (Access denied.)” appears and the job will not start.
12.5.8. Q. In the functions where a black console window appears, such as various functions of Winmostar or the execution of the solver, the processing of the black console window does not end and does not proceed.
12.5.9. Q. When I open a file or model a molecule, the bonds no longer appear or a lot of extra bonds have come to appear.
- In the case of Windows 7:
Press the Alt key.
Open View tab in menu
uncheck hide extensions for known files type
- For Windows 8, 10
Open View tab
Check File name extensions
12.5.11. Q. Markers (red circles) and group selections (blue circles) are not displayed. Atoms can no longer be selected.
12.6.1. Q. I cannot open files created by other than Winmostar with Winmostar. When I edit the file generated by Winmostar and try to open it with Winmostar, it cannot be opened.
——— Question details ———
generate.log and processing does not end normally.
gmx insert-molecules -try 100 -f gmx_tmp_water.gro -o gmx_tmp_water_tmp.gro -ci mol0.gro -nmol 64 ... set +v Error : Failed to solvate.
There are cases where the number of molecules is large (depending on the case, but it is about 10,000), since it is currently the limit of processing of gmx solvate, which is used in internal processing,.
In future it is also planned to handle cases where the number of molecules is large with this function.
12.8.2. Q. When executing parallel MPI of LAMMPS or Quantum ESPRESSO, warning is displayed as Unable to open the HKEY_LOCAL_MACHINE\SOFTWARE\MPICH\SMPD\process\???? registry key, error 5 , Access denied.
12.9.1. Q. Please tell me how to submit a job to a supercomputer or a linux server in my company or my campus.
12.10.1. Q. Is it possible to calculate the interaction between one substance and another substance with Winmostar?
12.10.2. Q. Can I calculate bond energies and bond divergence energies for a given bond in a molecule?
12.11.1. The Hamiltonian calculation method (Hamiltonian) or basis function (Basis Set) that I want to use is not found in the Configure window or the Easy Setup window for MOPAC, GAMESS, Gaussian and NWChem. How do I set it up?
If you can enter directly into the calculation method and basis function setting fields, you can do so directly with the keyboard. Different solvers may have different descriptions of polarization functions (represented by “*”, “p”, “d”, and “f”), so please check the manual for each solver.
12.11.4. Q. It will display abnormally with the message ATOMS **, **, AND ** ARE WITHIN. **** ANGSTROMS OF A STRAIGHT LINE displayed in the MOPAC log.
12.11.5. Q. When MOPAC is executed, “UNRECOGNIZED KEY - WORDS: (PM 6 (Hamiltonian name))” is output to the log and the calculation ends.
MOPAC which is included in Winmostar does not support the solvent effect (COSMO method). Please consider using GAMESS which is more accurate than MOPAC, although it takes more time to calculate.
12.11.7. Q. When I calculate with MOPAC other than Winmostar built-in (e.g. MOPAC2016), only some molecular orbitals are displayed.
Check the ALLVECS checkbox in the MOPAC Setup window to create an input file and perform the calculation.
12.11.9. Q. Is there a guideline for the maximum number of atoms (memory requirement) that can be calculated in GAMESS, Gaussian, and NWChem?
12.11.10. Q. Is it possible to speed up 3D display of ESP (electrostatic potential) of GAMESS, Gaussian, and NWChem?
12.11.11. Q. When running GAMESS, “* ERROR: MEMORY REQUEST EXCEEDS AVAILABLE MEMORY” etc. will be output to the log and the calculation will end abnormally.
12.11.12. Q. Immediately after installing GAMESS for Windows, I was able to use it without any problems, but at some point, all the calculations started to terminate abnormally in the middle. Is there a way to fix this?
12.11.13. Q. GAMESS outputs “WARNING. NUMBER OF INTERNAL COORDINATES IS GREATER THAN (3N - 6), BUT NO SYMMETRY COORDINATES ARE GIVEN.” in the calculation of only one atom and abnormally ends.
12.11.14. Q. The message
**** ERROR **** PCM SPHERE (S) MUST HAVE A POSITIVE RADIUS is displayed in the log of GAMESS and abnormally ends.
12.11.15. Q. When GAMESS is executed, “ERROR: BAD DELOCALIZED COORDINATES GENERATED !!!” is output to the log and the calculation ends abnormally.
In the GAMESS Setup, in the Basic tab, add ICUT=11 in the Others field in the $CONTRL box to make the cutoff value of the two-electron integral smaller (more severe).
12.11.18. Q. For some molecules, after optimization of Firefly, when I check the Molecular Orbit UVvis…, I get the error '*******' is not valid floating point value”.
12.11.19. Q. How do I deal with the message “THE GEOMETRY SEARCH IS NOT CONVERGED!” when I run a structural optimization calculation with GAMESS?
12.11.20. Q. When parallel execution of NWChem, the calculation outputs “Please specify an authentication passphrase for smpd:” to the log and dows not run.
12.11.21. Q. When I run NWChem, I get the message “sym_geom_project: sym_center_map is inconsistent with requested accuracy” in the log and the calculation does not run.
12.11.26. Q. I get an error when I try to load a Gaussian fchk file that is several GB in size and display molecular orbitals.
12.12.3. Q. In the MD calculation, how does the constraints by the SHAKE method etc. affect the calculation result? How do I choose a constraint method ?
12.12.4. Q. Why do molecules sometimes come out of the cell when in the trajectory or the final structure afterMD calculation?
12.12.5. Q. When I create a cell by adding water molecules from a cell in the [Solvate/Build Cell] menu to a large molecule such as a protein, the molecules sometimes stick out of the cell.
12.12.6. Q. In the [MD]-[Assign Charges Automaticcally] menu, the error message “Topology file not found” is displayed. Is there a solution?
12.12.7. Q. The process of assigning the force field takes a long time and never ends. Is there a solution?
Especially when GAFF or OPLS-AA/L+GAFF is selected as the type of force field, it may take a long time to process. This is caused by the fact that acpype is used to allocate GAFF, OPLS-AA/L+GAFF, and acpype processing is slow. In the case of macromolecules with nearly 10,000 atoms per molecule, we have confirmed that the process can be completed normally after about 5-6 hours. Depending on the environment, it may be faster than this, or conversely, it may be slower. In the future, Winmostar will work on speeding up the process of allocating these force fields.
12.12.9. Q. Can I calculate dielectric constant from Gromacs or LAMMPS (Molecular Dynamics Calculation)?
12.12.10. Q. When I try to run an MD calculation from a structure created with the interface builder, the force field assignment fails or the MD calculation fails. Is there a solution?
12.12.11. Q. When pressure control (constant NPT or NPH) is used, the calculation fails in the middle of the process. Is there a solution?
12.12.12. Q. How do I decide interaction parameters between liquid (organic) and solid (inorganic) in LAMMPS and Gromacs?
12.12.13. Q. When I load the final structure or animation from Gromacs, or when I edit it in some way and then run the MD calculation again, the force field assignment fails or the MD calculation breaks down. Is there a solution?
12.12.15. Q. Even if Gromacs ER method result loading is executed, the result can not be displayed / an error will appear.
12.13.1. Q. I installed the Quantum ESPRESSO pseudopotential file as per the instructions, but it is not recognized.
Au.pbe-dn-rrkjus_psl.0.1.UPF, etc.) to the pseudo folder under the Quantum ESPRESSO installation folder ( By default, this is C:\Program Files\Quantum ESPRESSO 64-bit 5.2.1pseudo etc.) under the Quantum ESPRESSO installation folder. However, if you download and save the UPF file using a browser such as the old Internet Exproler, there have been reports of problems such as the extension being changed without your permission, so please also try a browser such as Edge or Chrome.