12. Frequently asked questions · Troubleshooting

12.1. Purchase

12.1.1. Q. Please tell me how to pay the price.

A.
[For corporations]
It becomes postpay under the following conditions.

Payment method: Cash transfer to our designated bank account
Payment due date: End of the next month of the purchase date

[For individuals]
Pay with credit card at PayPal.

12.1.2. Q. Please tell me the types of documents issued by the company.

A.
An invoice, a delivery note and a quotation will be issued.
In the case of PayPal, please obtain a receipt from PayPal.
Please consult us when you wish other documents. However, please understand that it may be refused depending on the matter.

12.1.3. Q. How do I place an order other than an end user, such as an agency?

A.
Please use a designated agent. For more information, please visit Pricing.

12.2. License Code

12.2.1. Q. Is it possible to change the registered user of a specific user license?

  1. 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?

  1. If you move from your institutional affiliation at the time of purchase, you cannot use it, even if it is a permanent right.

12.2.3. How do I change an already entered license code?

Enter the license code you want to use from now on into license code in Tools ‣ Preferences menu.
If you are a student and want to switch from the free version to the student version, check the student version on the License registration page and register the license again.

12.2.4. Q. Please tell me how to display the MAC address.

A. In Windows 10, start the command prompt by clicking on Start menu ‣ Windows System Tools ‣ Command Prompt. Then, in a command prompt window, type ipconfig /all and press the Enter key. Look for the “Physical Address” line among the various information that will be output. That content is 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.

12.2.5. Q. Does Winmostar license fee include Gaussian license fee, and is there a Winmostar lineup with Gaussian license?

A. Winmostar license fee does not include Gaussian license fee. There is no Winmostar lineup with Gaussian license. Please purchase it separately from Gaussian distributor.

12.3. Support and Maintenance

12.3.1. Q. Can I get support for bugs or patches?

This will be done in accordance with the terms of use. The latest terms of use are here ( Winmostar V10 Terms of Use ).

12.3.2. Q. How long do you plan to support and maintain the previous version?

  1. Based on the terms of use in effect for your version of Winmostar. In addition, simple instructions on how to operate the system will be provided to the extent possible.

12.3.3. Q. Can I get in touch with the manufacturer directly?

  1. You can contact us through the contact form, but our availability is subject to our terms and conditions. The latest terms of use are here ( Winmostar V10 Terms of Use ). You can use paid support for more advanced email support.

12.3.5. Q. Is it possible to update/upgrade version of the Winmostar I am using?

A. Minor version (and revision) updates can be done as many times as you like during the availability period. Renewal of a major version requires renewal of the license for a permanent license, and is enforceable for an annual license.
As an example, for “V8.039”, “8” refers to the major version and “039” to the minor version. For V9.1.0, “9” refers to the major version, “1” to the minor version, and “0” to the revision.
For example, a perpetual licensee of Winmostar V9 can update from V9.1.0 to V9.1.5 or V9.4.4, but it is not possible to update to V10.0.0.

12.3.6. Q. Are there any precautions when asking a question?

A. If you have a question that the calculation does not work properly, please send us an input or output file that reproduces the situation in principle.

12.4. Functions and use of the software

12.4.1. Q. Does Winmostar connect to internal and external servers or the cloud, or can it be used without a LAN connection?

A. Yes, it is possible. Download the software described in Installing Winmostar and solvers and copy it to a PC not connected to the network. Then, follow the procedure in Installing Winmostar and solvers to install the software.

12.4.4. Q. Do you have any calculation software installed on Winmostar itself?

A. Only MOPAC and CNDO/S are installed in Winmostar. Other software is not bundled with Winmostar due to licensing issues and must be installed separately. Many software can be installed for free, and the instructions are described in Installing Winmostar and solvers.

12.4.5. Q. Do you let Winmostar run calculations in the cloud?

A. It is possible to have it calculated in the cloud, or not. By default, we don’t use the cloud, but let you run the calculations on a Windows PC with Winmostar installed.

12.4.6. Q. Does Winmostar support GPU computation?

A. GPU computation is supported, but the default configuration is not to use GPU; GAMESS, Gaussian, Gromacs, LAMMPS, and Quantum ESPRESSO support GPU, but you will have to pay to check and configure them.

12.4.8. Q. Is it possible to do parallel computation using Winmostar?

A. Yes, it is possible. For details, please refer to the keyword setting window page for each solver.

12.4.9. 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?

A. You can specify an unlimited number of parallels within the range of user-provided hardware. Winmostar’s price does not change depending on the number of parallels. In the case of a local job, change the maximum number of cores because the job will not run if it exceeds the maximum number of cores set by Winmostar Job Manager.

12.5. Software operations

12.5.1. Q. I can not create a model as I expected. It can not calculate. It does not work.

  1. 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, 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)
Next, please make it possible to record subsequent work with Notepad etc. If you find out how to reproduce the problem, you may be able to fix it in a relatively short time if you report along with the record of work.
Please trace the basics tutorial of the solver you want to use in tutorials.
If you fail to trace the basics tutorial, try the following.
  • 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 CygwinWM, and solvers including MPI from monitoring.
  • If you are using CygwinWM, run Help ‣ Check cygwin_wm and 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.

12.5.2. Q. “ERROR: I/O error 32” is displayed and the processing fails.

A. The file related to processing may be opened by an application or process other than Winmostar, locked, or it may have been deleted.
Restart OS and try again in the situation other applications are not open.

12.5.3. Q. Process using Cygwin will end abnormally. / tools ‣ diagnose cygwin_wm 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.

  1. Perform general dealing with common problems.
  2. Restart your PC
  3. Search and delete anything other than cygwin1.dll and restart the machine

Warning

  • This operation is necessary in some cases if cygwin1.dll exists in addition to CygwinWM on the same machine.
  • cygwin1.dll may be included in various freeware etc even if you do not install Cygwin in other location.
  1. 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.
  2. 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).
  3. Temporarily disable security software.
  4. Disable software that tends to cause problems described in Cygwin FAQ .
  5. In addition, try the method described in Cygwin FAQ fork() related failures.
  6. Install a new version of Cygwin from the Cygwin official site and check if you can start a terminal.

12.5.4. Q. Tools ‣ Check cygwin_wm function will display WARNING … some files are missing.

A. Please reinstall CygwinWM.
If it is displayed even after the reinstallation, temporarily disable the security software, or exclude installation destination and installer from monitoring.

12.5.5. The job registered in Job Manager is not executed.

If the specified parallel number of MPI is larger than the MaxCore setting of Job Manager, the job will not be executed.
The default value of MaxCore should be set to the number of cores of the running PC, but make sure that it has not been changed or that the number of parallel MPIs has not been set higher.
If you want to run without using Job Manager, uncheck “Run MOPAC using Job Manager” or “Run the other solvers using Job Manager” in Calculation tab of the Tools ‣ Preferences window.

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.

A. If you happen to click on the black console window, the process will be suspended from there due to the Windows specification.
The processing will resume when ESC key is pressed while the console window is active.

12.5.7. 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.

A. The value of Bonding factor in Tools ‣ Preferences ‣ Edit may not be appropriate. Return to the default value or set a value around 1.15.

12.5.8. Q. How do I view the extension in Windows Explorer?

In the case of Windows 7:
  • Open Explorer
  • Press the “Alt key.
  • Open View tab in Tools ‣ Folder Options menu
  • uncheck hide extensions for known files type
For Windows 8, 10
  • Open Explorer
  • Open View tab
  • Check File name extensions

12.7. On the modeling of molecules and creation of systems

12.7.1. Q. How do I change the type of chemical bond (single, double etc.)?

A. You can change it by the following method, for example.
1) Edit ‣ Automatically Adjust Atoms/Bonds ‣ Add/Change Bond or by pressing the Add/Change Bond button at the top of the main window multiple times.
2) Edit ‣ Automatically Adjust Atoms/Bonds ‣ Regenerate All Bonds is selected, the type of chemical bond is automatically changed by the bond degree determined from the interatomic distance. If you optimize the structure with Edit ‣ Automatically Adjust Atoms/Bonds ‣ Quick Optimization in advance, it may be changed automatically more reasonably.
3) If only one small molecule is displayed, execution of MOPAC calculation will automatically change the coupling order using the population analysis result.

12.7.2. Q. MD ‣ Solvate/Build Cell function will display Error: Failed to solvate. and processing will fail.

——— Question details ———

When executing MD ‣ Solvate/Build Cell, the following is output to 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.

  1. Comment out or delete the line of
source /usr/local/gromacs_sse/bin/GMXRC

Or

source /usr/local/gromacs_avx/bin/GMXRC

in /etc/profile.d/winmostar.sh under CygwinWM installation folder.

  1. Click Tools ‣ Cygwin of Winmostar and try 1-2. Gromacs of Installation procedure of solvers for Winmostar on the installed cygwin.
  2. Click Tools ‣ Cygwin and 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, Edit ‣ Modify Selected Group ‣ Replicate.

In future it is also planned to handle cases where the number of molecules is large with this function.

12.8. MPI on local machine, parallel execution

12.8.1. Q. MPICH ends during computation.

——— Question details ———
While executing MPICH, the following error may be displayed and the calculation may be ended prematurely.
op_read error on left context: Error = -1
op_read error on parent context: Error = -1
unable to read the cmd header on the left context, Error = -1
unable to read the cmd header on the parent context, Error = -1
Error posting readv, An existing connection was forcibly closed by the remote host.(10054)
connection to my parent broken, aborting.
state machine failed.

A.
This error is because MPICH uses the network adapter even if it is localonly and the network adapter is disconnected in the middle.
However, if the network adapter has disconnected from the beginning, this error will not occur because MPICH does not use the network adapter.
When computing for a long time using MPICH, please disable the network adapter and start the calculation.

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.

A. MPICH tries to rewrite the registry but it failed because there is no administrator authority.
If you start Winmostar with administrator privileges, you will not get a message. Even when a message is displayed, the calculation itself is executed normally, so it can be ignored.

12.9. Remote Jobs

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.

A. If you need environment settings specific to the computer to which you are connecting, you can do it by creating a template script for remote jobs.
See Remote job for more information.

12.9.2. Q. The connection test with Test Connection succeeds, but the job submission fails.

A. There are various reasons. Here are some examples

1. If there is a limit on the number of SSH connections such as TSUBAME3.0, please consult us to avoid it without executing SSH connection every time.
2. In some cases, this can be avoided by activating password authentication as well as secret key authentication on the server side.
3. If there are multiple login server entities and they are automatically selected in the background, you may be able to avoid this by using only a specific login server or connecting until all servers are registered in the cache .
4. Even if Winmostar submits a job submission command (such as qsub) from the local machine, the command may not be found on the remote server. This can be avoided by filling Profile –> Edit Profile…’ in the :guilabel:`Submit Remote Job window with the path of an executable such as qsub. To avoid this problem, add the path of an executable such as qsub to Prefix for queueing commands of Profile –> Edit Profile… in the Edit Profile. For example, if the full path of :command:`qsub is /usr/local/bin/qsub, type “/usr/local/bin/” in Prefix for queueing commands.

12.9.3. Q. The connection test with Test Connection succeeds, but the job submission fails.

——— Question details ———
Even though the result of TestConnection is OK, various commands can not be executed.
And the following dialog is displayed at the time of launching remote job submission window or TestConnection etc.
WARNING: Putty default host name was found in registry.
(\SOFTWARE\SimonTatham\PuTTY\Sessions\Default%20Settings\HostName)
This may cause errors while job submission.
Clear this setting.

A.
Reason:
This WARNING occurs when Putty's HostName is set.
Since Putty's settings are saved in the Windows registry, even if the Putty is other than Winmostar bundled version, this problem will occur when some sort of character string is saved in HostName.
Solution:
Launch Putty from Connection ‣ Open Putty Remote Job Submit window. Check a character string is set in the HostName field of Default Settings.
You can solve this problem by deleting this string and saving it with Default Settings selected.
(The input contents in the Port column are not particularly affected.)

12.10. MOPAC, CNDO/S, GAMESS, NWChem, Gaussian

12.10.1. Q. How many atoms can be calculated with MOPAC?

A. 70 heavy atoms (other than hydrogen) and 90 light atoms (hydrogen).
You can also download the executable binary of MOPAC6 for large molecules (up to 420 atoms) from the here <https://winmostar.com/jp/mop6wxxx.zip>.
Winmostar also supports MOPAC2016.
MOPAC2016 has no limit on the number of atoms, and is free for those who belong to a institution for academic degrees.
MOLSIS web page <https://www.molsis.co.jp/en/>

12.10.2. Q. It will display abnormally with the message ATOMS **, **, AND ** ARE WITHIN. **** ANGSTROMS OF A STRAIGHT LINE displayed in the MOPAC log.

——— Question details ———
It stops with an error saying that 3 atoms are linear as shown below.
CALCULATION ABANDONED AT THIS POINT

THREE ATOMS BEING USED TO DEFINE THE
COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS
NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT
LINE. THERE IS A HIGH PROBABILITY THAT THE
COORDINATES OF THE ATOM WILL BE INCORRECT.
THE FAULTY ATOM IS ATOM NUMBER 69
Finally, comes
ATOMS 68, 57, AND 54 ARE WITHIN .0134 ANGSTROMS OF A STRAIGHT LINE
.

A.
It is displayed when an angle close to 180 degrees is included in Z-Matrix.
Change the connectivity of atoms by the coordinate editing function in the lower right of the main window so that there is no angle close to 180 degrees from Z-Matrix.
If you are new to Z-Matrix, you may be able to avoid this error by adding “XYZ” to the keyword as a different method.
Alternatively, by adding a dummy atom of the atomic type XX to a position out of the line where three atoms are aligned in a straight line and designating it as a connection destination on the Z-Matrix of the atoms arranged in the line,
Sometimes it is possible to avoid errors.

12.10.3. Q. When MOPAC is executed, “UNRECOGNIZED KEY - WORDS: (PM 6 (Hamiltonian name))” is output to the log and the calculation ends.

A. If you can avoid the error by changing Hamiltonian to AM1 with MOPAC Configure, the selected Hamiltonian is not supported by the MOPAC you are using.
Check the list of Hamiltonians supported by each version and select the appropriate Hamiltonian.
If it still does not work, please take action of general errors .

12.10.4. Q. It can not be calculated when Method=INDO is used in CNDO/S.

A. The elements after F are not supported by Method=INDO.
set Method=CNDO, or use a non-empirical solver such as GAMESS.

12.10.5. Q. Is it possible to speed up 3D display of ESP (electrostatic potential) of GAMESS, Gaussian, and NWChem?

A. If you have installed the Windows version of Gaussian, check the Cubegen check box in the Cubegen window that appears when you open the Cube file, and the processing will be relatively fast using the Cubegen program included with Gaussian.
In the future, we plan to speed up the cube file processing program (OpenCubegen) included with Winmostar.

12.10.6. Q. I can not run NMR calculation with GAMESS.

A. First of all, please take action of general errors.
It is necessary to set DIRSCF=.F. in $SCF and NCPUS=1 because parallel calculation is not supported.
(The details are listed as follows at the end of the calculation result output.)
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.

12.10.7. Q. When running GAMESS, “* ERROR: MEMORY REQUEST EXCEEDS AVAILABLE MEMORY” etc. will be output to the log and the calculation will end abnormally.

A. It means that the allocated memory capacity of GAMESS is insufficient.
You can avoid errors by increasing the value of MWORDS in the input file.

12.10.8. 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.

A. This is a message indicating a problem caused by using Z-Matrix in a system with only one atom.
In this case, Cartesian coordinates are used (COORD=UNIQUE) to solve it.
Set UNIQUE to COORD on Wimostar's GAMESS Configure window.

12.10.9. Q. The message **** ERROR **** PCM SPHERE (S) MUST HAVE A POSITIVE RADIUS is displayed in the log of GAMESS and abnormally ends.

A. GAMESS may not contain Cavity radius for some atoms.
To specify the Cavity radius, add the following statement just after the $PCM line.
$PCMCAV RIN(13)=1.55, RIN(15)=1.55 $END
In this example, Cavity radius is set to the 13th and 15th atoms.

12.10.11. Q. When parallel execution of NWChem, the calculation outputs “Please specify an authentication passphrase for smpd:” to the log and dows not run.

A. If you omit the pass phrase (passphrase) when installing MPICH 2, such an error may occur.
There are several solutions, but after uninstalling MPICH2, reinstalling MPICH 2 may resolve it.
In that case, you need to stop smpd before uninstalling MPICH2 and install smpd after reinstalling MPICH2.

12.10.12. Q. I read the Gaussian out file, but the orbital (eigen) energy etc. are not written.

A. It is not output if pop=full or pop=regular is missing in the Gaussian input file.

12.10.13. Q. How do I calculate the chk file read in Gaussian?

A. For remote jobs, check [Advance] in the SubmitJob window and uncheck [Delete *.chk] to leave the chk file. And the chk file is loaded and the calculation runs when the same name was used.
The method using –Link1– is simpler in setting itself, so please consider using it as well.

12.10.14. 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”.

A. The linear dependence of the basis is large because 6-31+G* has the diffuse functions.
Therefore, a part of the value of the molecular orbital coefficient becomes very large, and **** is output in the log.

The solutions are
1. Use 6-31G* basis set
2. If you use 6-31+G*, use GAMESS instead of Firefly
.

Because GAMESS has processing of linear dependency,
Firefly and GAMESS may have slightly different energy values.
execute a series of calculations with either Firefly or GAMESS.

12.11. Gromacs, LAMMPS

12.11.1. Q. How can we equilibrate the system in molecular dynamics calculation?

A. First of all, describing the case where the calculation of the aggregation system (liquid and solid, not gas) of the equilibrium state of low molecular is target.
When aligning molecules in the initial state, please set the density as close as possible to the final density.
However, when it is not possible to arrange it unless it is considerably low density, it does not matter.
After that, please carry out energy minimization, constant temperature calculation, constant temperature pressure calculation until the change of the potential energy, temperature and density converge.
If the initial density is too low, compress it with a pressure higher than the target pressure (for example, about 100 times) by constant temperature pressure calculation.
Finally, if you are interested in the ensemble average physical quantity and reaching the target temperature and pressure after equilibration, the difference in the fine equilibration procedure is less likely to have a significant influence on the calculation result.
In the case of polymers and glasses, in most cases it is impossible to obtain an equilibrium state in a real sense, because realistic computation time is almost impossible, so the convergence of energy, temperature and density, the influence on the physical quantity to be observed is affected Equilibrium calculation is carried out for a time to the extent that the correlation of physical quantities considered to be large reaches zero.
Since pressure control is unstable in the case of gas, equilibrium state is obtained only by energy minimization and constant temperature calculation.

12.11.2. Q. Even if Gromacs ER method result loading is executed, the result can not be displayed / an error will appear.

A. Please check the contents of ermod.out generated in the output destination directory specified when executing the ER method.
If it says “The minimum of the energy coordinate is too large” in ermod.out, press the [Options] button on the ER method execution window and select [For Solution System] Please reduce the value of [minimum value of the solute - solvent energy (ecdmin)].
For details on how to set concrete values, please see ERmod wiki FAQ.
Similarly, check the contents of ermod.out and ERmod wiki FAQ and if you need to change the setting of ermod, set it in [Options] of ER method execution window.

12.11.3. 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 ?

A. The SHAKE, RATTLE, LINCS, and SETTLE methods are applied between atoms that are covalently bonded to restrict the bond length, so that the time step can be increased and even longer computations can be performed more stably with the same amount of computation. “Stable” is in terms of Hamiltonian (total energy) conservation.
Functions that express covalent bonds when not constrained also do not accurately represent actual phenomena. Therefore, assuming that stable calculations are being performed, there are deviations from the actual phenomena due to the respective circumstances both in the case of restraining and in the case of not restricting, in terms of the effect on various calculated physical properties.
Unless the vibrational motion in the molecule itself has the purpose of calculation, it is basically recommended to select the condition that the Hamiltonian preserves for a long time in each case.
However, if the bonds of the hydrogen atoms are not constrained, the atoms will move at high speed significantly in the system, which may cause the drift of the Hamiltonian. Therefore, in many cases, the bonds of the hydrogen atoms are constrained.

12.11.4. Q. Why do molecules sometimes come out of the cell when in the trajectory or the final structure afterMD calculation?

A. Using periodic boundaries, the entity of the molecule should be inside the cells of the periodic boundaries.
But, solvers such as Gromacs and LAMMPS record trajectories with translational values as they are without folding coordinates even when molecules cross over cell boundaries to calculate mean square displacement, etc.
Either way, the result will be properly considered and the same result will be output during the result analysis, so there is no effect on the result analysis.
If the appearance of molecules jumping out of the cell is not good, adjust the settings of View - Wrap Around Cell Boundary.

12.11.5. Q. Can I calculate dielectric constant from Gromacs or LAMMPS (Molecular Dynamics Calculation)?

A. Since the dielectric constant is a physical property dependent on the frequency of the external field, and the mechanism is different for each frequency band, we cannot answer them all.
The dielectric constant calculated from Winmostar’s Gromacs and LAMMPS is a component derived from molecular orientation on the assumption that intramolecular polarization does not change with time.
And among them, it is the infinitely slow low frequency limit value calculated from the fluctuation of the dipole moment of the whole system within the simulation time of molecular dynamics calculation.
Be careful for substances with large molecular weights and slow relaxation, such as polymers, because only information within the range that can be observed within the simulation time is known.
The dielectric function calculated from Winmostar’s Quantum ESPRESSO is the dielectric function of the high frequency component derived from the polarization of the electron with the atomic coordinates fixed.
It is necessary to plan the calculation considering how to obtain the experimental value of the dielectric constant to be compared, the properties of the material, and the research purpose.
In addition, it is possible to help with planning with our paid support.

12.11.6. Q. When loading the final structure or animation in Gromacs, the molecules are sometimes displayed in pieces.

A. This problem is caused by a minor bug in Gromacs. Considering the periodic boundary condition, the shape of the molecule is maintained, and it is properly processed as a molecular dynamics calculation, so there is no problem in analyzing the results. To modify the appearance, select display ‣ periodic boundary condition format to relocate atomically inside the cell.

12.11.7. Q. When pressure control (constant NPT or NPH) is used, the calculation fails in the middle of the process. Is there a solution?

A. First of all, in a situation where the interaction between molecules is extremely weak, such as in the gas phase or when other phases are dispersed in the gas phase, the pressure control is not stable, so try a method without pressure control. Next, look at the change in density over time in the broken calculation to see what’s going on. Also, the energy, temperature, and pressure must be sufficiently equilibrated at a constant density before pressure control can be performed. At the end of equilibration at constant density, the pressure (the mean value of) is preferably 0 or negative. If the pressure value is large at the end of equilibration at a constant density, the system size will change drastically immediately after starting pressure control. If you want to reduce the pressure at the end of equilibration at a constant density, reduce the initial density. If this does not solve the problem, (1) change the pressure control to Berendsen method instead of Parrinello-Rahman (Nose-Hoover) method, (2) increase the time constant of the pressure control, and (3) divide the calculation with the pressure control into several short calculations.

12.12. About Quantum ESPRESSO, OpenMX

12.12.2. Q. Calculation using Quantum ESPRESSO fails. An error appears in displaying the calculation result.

A. First of all, please take action of general errors.
Next, since Winmostar continuously executes each module of QE by batch processing, we look at the flow of processing described in Winmostar generated bat file (local execution) or sh file (remote execution) While checking the generated output file (pwout or out) file in order.
For example, check ph.x output log (ph.out) for phonon calculation.
Please take action on the place where error such as “Error in routine …” appears first, then execute the job again.
Errors related to specific keywords, please confirm the setting of that keyword official site <https://www.quantum-espresso.org/Doc/INPUT_PW.html>.
Typical QE error handling is described in official site FAQ <http://www.quantum-espresso.org/resources/faq>.

12.12.4. Q. Quantum ESPRESSO, OpenMX SCF calculation or structure optimization calculation does not converge.

A. Please carry out the following countermeasures in order.
Always to try:
· First-principles calculations have many setting items, so do not change the calculation conditions appropriately, and stream a series of calculations while recording properly.
Take action for general problem of QE.
· Check if it tends not to converge really.
· Plot the Estimated accuracy against the number of SCF cycles for QE. It is still good if it is a log-log plot.
· Spin Polarization State · Determine whether electric charge is appropriate.
· If you shift K_POINTS in Hexagonal crystal, remove the shift.
· Gives the order of up/down spins.
· Constrain the magnetic moment of the whole system.
· Use a reasonable initial structure.
· Use structures obtained by experiments and other calculation methods.
· If there are arbitrary atoms (placement of light elements, solid solutions, defects, non-integral components etc. which can not be seen with X rays) in the calculation, try different arrangements.
· In cases where solid solution · defects are included, make the initial structure so that large dipole moment does not occur in the system.

Try next:
· Adjust mixing_mode.
· If you are not using smearing, use smearing.
· Change the type of pseudopotential.
· Adjust the initial value of spin polarization. (Atomic unit or whole system)
· If relatively complicated conditions such as external electric field, defect, adsorption, etc. are set, try them under simpler conditions than eliminating them, and if the calculation converges, the final state of the calculation (atomic arrangement · wave function Etc.) as the initial state and starts the calculation.

· Calculation is started from halfway of computation that did not converge (SCF algorithm depends on history).
· Adjust the parameters of matrix calculation (review only settings that are difficult to converge).
· If large dipole moment occurs in the system, such as molecules are adsorbed on the slab, correct the dipole.

Try in balance with calculation time / calculation precision:
· Take a large cutoff energy.
· Take a lot of K points.
· Adjust smearing (type / width).
· Reduce the degree of update of the wave function (mixing_beta in QE).

Try with balance with calculation accuracy:
Loosen the convergence parameter of the SCF.

12.12.5. 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.

A. First of all, please check nbnd description of the QE official manual.
If you do not use nbnd when you do the calculation, QE automatically calculates nbnd by setting it automatically, so please uncheck “Use nbnd” on the keyword setting screen of Winmostar.
To increase nbnd, set nbnd to a value larger than the value of “number of Kohn-Sham states” that is output to the pwout or out file when executed without using nbnd.
Also please refer to the value of “# valence bands:” displayed at “Use nbnd” on Configure window of Winmostar (See Solid ‣ Quantum ESPRESSO menu for detail).

12.12.7. Q. The SCF calculation of Quantum ESPRESSO on metal is terminated abnormally with “charge is wrong” displayed in the output file (.pwout or .out). How do I resolve this?

A. First, make sure that the occupations are set to smearing, and then set the ectrho to a larger value (such as 400 Ry).

12.12.11. Q. When I try to output the Fermi surface, they do not appear.

A. First, make sure that the target substance is a metal. Next, output the density of states, and confirm that the density of states is not 0 on Fermi energy.

12.12.13. 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.

A. For issues specific to Cygwin’s OpenMPI, go to Windows Settings - Network and Internet - Change Adapter Options and disable the network adapter you are not using. Also, OpenMX recommends that you use OpenMP on the local machine.

12.12.14. Q. How do you set up the type of functionalities in Quantum ESPRESSO?

A. In Quantum ESPRESSO, since a pseudopotential file is created for each function, the function is basically determined when the pseudopotential file is selected. Some functions (e.g., HSE, vdw functions) select the pseudopotential file created by the base function (e.g., PBE in the case of HSE) and then use the input_dft keyword to override the function’s settings.

12.13. Addons

12.13.1. 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.

A. It is because of the group contribution algorithm implemented. When searching for an atomic group, the search is started from the largest atomic group. It is recommended that functional groups that seem to be important be included in the repeating unit.

12.13.2. Q. The value of the Hansen solubility parameter obtained using the solubility parameter calculation module is significantly different from the literature value.

A. The solubility parameter calculation module outputs Hansen solubility parameters using the group contribution method trained by the neural network using various literature values as learning data. Therefore, it does not return exactly the same value as the literature value. Please note that the unit of the solubility parameter differs depending on the literature.