12. Frequently asked questions · Troubleshooting¶
- License Code
- Q. Is it possible to change the registered user of a specific user license?
- Q. If I move from the institution where I purchased my educational license to another institution, can I continue to use that license?
- How do I change an already entered license code?
- Q. Please tell me how to display the MAC address.
- Q. Does Winmostar license fee include Gaussian license fee, and is there a Winmostar lineup with Gaussian license?
- Support and Maintenance
- Q. Can I get support for bugs or patches?
- Q. How long do you plan to support and maintain the previous version?
- Q. Can I get in touch with the manufacturer directly?
- How to pronounce Winmostar.
- Q. Is it possible to update/upgrade version of the Winmostar I am using?
- Q. Are there any precautions when asking a question?
- Functions and use of the software
- Q. Does Winmostar connect to internal and external servers or the cloud, or can it be used without a LAN connection?
- Q. Please tell me the minimum and recommended specifications of PC for Winmostar.
- Q. Is it possible to use the created molecular model etc for academic presentations and papers? How should I quote at conference presentations and paper submissions?
- Q. Do you have any calculation software installed on Winmostar itself?
- Q. Do you let Winmostar run calculations in the cloud?
- Q. Does Winmostar support GPU computation?
- Q. Which CPU is more suitable for operation, Intel or AMD? Which one would you recommend?
- Q. Is it possible to do parallel computation using Winmostar?
- Software operations
- Q. I can not create a model as I expected. It can not calculate. It does not work.
- Q. “ERROR: I/O error 32” is displayed and the processing fails.
- 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 will display WARNING … some files are missing.
- The job registered in Job Manager is not executed.
- 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. 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.
- 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.
- Q. How do I view the extension in Windows Explorer?
- On the modeling of molecules and creation of systems
- Q. How do I change the type of chemical bond (single, double etc.)?
- Q. function will display Error: Failed to solvate. and processing will fail.
- MPI on local machine, parallel execution
- Remote Jobs
- MOPAC, CNDO/S, GAMESS, NWChem, Gaussian
- Q. How many atoms can be calculated with MOPAC?
- Q. It will display abnormally with the message ATOMS **, **, AND ** ARE WITHIN. **** ANGSTROMS OF A STRAIGHT LINE displayed in the MOPAC log.
- Q. When MOPAC is executed, “UNRECOGNIZED KEY - WORDS: (PM 6 (Hamiltonian name))” is output to the log and the calculation ends.
- Q. It can not be calculated when Method=INDO is used in CNDO/S.
- Q. Is it possible to speed up 3D display of ESP (electrostatic potential) of GAMESS, Gaussian, and NWChem?
- Q. I can not run NMR calculation with GAMESS.
- Q. When running GAMESS, “* ERROR: MEMORY REQUEST EXCEEDS AVAILABLE MEMORY” etc. will be output to the log and the calculation will end abnormally.
- 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.
- Q. The message
**** ERROR **** PCM SPHERE (S) MUST HAVE A POSITIVE RADIUSis displayed in the log of GAMESS and abnormally ends.
- Q. When GAMESS is executed, “ERROR: BAD DELOCALIZED COORDINATES GENERATED !!!” is output to the log and the calculation ends abnormally.
- Q. When parallel execution of NWChem, the calculation outputs “Please specify an authentication passphrase for smpd:” to the log and dows not run.
- Q. I read the Gaussian out file, but the orbital (eigen) energy etc. are not written.
- Q. How do I calculate the chk file read in Gaussian?
- 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”.
- Gromacs, LAMMPS
- Q. How can we equilibrate the system in molecular dynamics calculation?
- Q. Even if Gromacs ER method result loading is executed, the result can not be displayed / an error will appear.
- 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 ?
- Q. Why do molecules sometimes come out of the cell when in the trajectory or the final structure afterMD calculation?
- Q. Can I calculate dielectric constant from Gromacs or LAMMPS (Molecular Dynamics Calculation)?
- Q. When loading the final structure or animation in Gromacs, the molecules are sometimes displayed in pieces.
- Q. When pressure control (constant NPT or NPH) is used, the calculation fails in the middle of the process. Is there a solution?
- About Quantum ESPRESSO, OpenMX
- Q. I don’t know how to find a pseudopotential file for Quantum ESPRESSO. How do I find them?
- Q. Calculation using Quantum ESPRESSO fails. An error appears in displaying the calculation result.
- Q. When executing Phonon calculation using Quantum ESPRESSO, “third order derivatives not implemented with GGA” is output in the ph.x output (ph.out), and the calculation result cannot be obtained.
- Q. Quantum ESPRESSO, OpenMX SCF calculation or structure optimization calculation does not converge.
- Q. The SCF calculation of Quantum ESPRESSO is displayed as “too few bands” in the output file (.pwout or .out) and abnormally ends. I do not know how to set nbnd.
- Q. When calculating the dielectric function using Quantum ESPRESSO, “bad band number” is displayed in the epsilon.x output (eps.out) and it is not possible to acquire the dielectric function.
- 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. When executing Phonon calculation using Quantum ESPRESSO, ph.x output (ph.out) displays “The phonon code with US-PP and raman or elop not yet available” and the calculation result can not be acquired .
- Q. When I try to output the Fermi surface, they do not appear.
- Q. Can I calculate the dielectric constant from Quantum ESPRESSO (band calculation)?
- Q. When I run a calculation on a local machine with MPI enabled in OpenMX, I get the error tcp_peer_send_blockingfr_to-socket 12 failed to send(): Transport endpoint is not connected.
- Q. How do you set up the type of functionalities in Quantum ESPRESSO?
- 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.
- Q. The value of the Hansen solubility parameter obtained using the solubility parameter calculation module is significantly different from the literature value.
- 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 move from your institutional affiliation at the time of purchase, you cannot use it, even if it is a permanent right.
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.
12.2.5. Q. Does Winmostar license fee include Gaussian license fee, and is there a Winmostar lineup with Gaussian license?¶
12.4.3. Q. Is it possible to use the created molecular model etc for academic presentations and papers? How should I quote at conference presentations and paper submissions?¶
- 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 cygwin_wm 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, 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 Winmostar.
- Restart the OS.
- With security software, Exclude Winmostar, installation folder of cygwin_wm, and solvers including MPI from monitoring.
- If you are using cygwin_wm, run and perform a simple diagnosis of cygwin_wm.
- Reinstall Winmostar, cygwin_wm 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
- Search and delete anything other than
cygwin1.dlland restart the machine
- This operation is necessary in some cases if
cygwin1.dllexists in addition to cygwin_wm 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 cygwin_wm is installed in
C:\cygwin_wm), execute the /bin/rebaseall -v, and restart the machine.
- 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).
- 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.
12.5.4. Q. function will display WARNING … some files are missing.¶
12.5.6. 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.¶
12.5.7. 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.¶
12.5.8. 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:
- Open Explorer
- Press the “Alt key.
- Open View tab in menu
- uncheck hide extensions for known files type
- For Windows 8, 10
- Open Explorer
- Open View tab
- Check File name extensions
12.6.2. Q. function will display Error: Failed to solvate. and processing will fail.¶
——— 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.
A. Try general errors and Cygwin general errors and execute after reducing the number of molecules or reducing the density. If you still can not do it, reinstall internally used Gromacs in the following procedure.
- Comment out or delete the line ofsource /usr/local/gromacs_sse/bin/GMXRC
/etc/profile.d/winmostar.shunder cygwin_wm installation folder.
- Clickof Winmostar and try
1-2. Gromacsof Installation procedure of solvers for Winmostar on the installed cygwin.
- Clickand run gmx. Rebuild will be successful if a message indicating GROMACS: gmx, VERSION …, etc. is displayed.
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.
12.7.2. 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.¶
12.8.1. Q. Please tell me how to submit a job to a supercomputer or a linux server in my company or my campus.¶
12.9.2. Q. It will display abnormally with the message ATOMS **, **, AND ** ARE WITHIN. **** ANGSTROMS OF A STRAIGHT LINE displayed in the MOPAC log.¶
12.9.3. Q. When MOPAC is executed, “UNRECOGNIZED KEY - WORDS: (PM 6 (Hamiltonian name))” is output to the log and the calculation ends.¶
12.9.5. Q. Is it possible to speed up 3D display of ESP (electrostatic potential) of GAMESS, Gaussian, and NWChem?¶
INCOMPATIBLE OPTION CHOSEN WITH RUNTYP=NMR *** NMR MAY BE COMPUTED ONLY FOR SCFTYP=RHF, NO CORRELATION OPTION (DFTTYP, CITYP, CCTYP, MPLEVL) MAY BE CHOSEN NO SEMI-EMPIRICAL OPTION (GBASIS=AM1/PM3/MNDO) MAY BE CHOSEN DIRECT AO INTEGRAL CALCULATION (DIRSCF) IS NOT ENABLED, AND/OR PARALLEL EXECUTION IS NOT ENABLED.