8.3. Towhee
Menu about Towhee.
8.3.1. Assigning force fields
If you are performing a Gibbs Ensemble Monte Carlo (GEMC) or Grand Canonical Monte Carlo calculation, the main window must be in animated view at this point and the number of frames in the animation must be 2.For GEMC, the first phase must have been created on the first frame and the second phase on the second frame.In the case of GCMC, the system to be calculated must be created in the first frame and the molecules not included in the first frame must be created in the second frame.
Sets the force field. The options change depending on the type of solver.
After assigning a forcefield, use Get Info to check the assigned forcefield.
In the case of LAMMPS, if a gro file with velocities is open in the main window at the time this feature is used, it will generate a data file with velocities.Similarly, in the case of Gromacs, if a data file containing velocity is open, a gro file containing velocity is generated.This is useful when you want to take over Gromacs and LAMMPS computed data with velocities.
Once you assign a force field and run the MD calculation, the bond order is automatically determined from the equilibrium length of the force field parameters.Depending on the type of force field, the bond order determined at that time may be different from the bond order before the force field assignment.Some force fields are affected by the bond order. Use Overwrite Bonds from File if you want to return to the bond order before force field assignment.
- Assign parameters automatically
Assign new force field parameters. Structures connected to each other by bonds in the molecule display area will be recognized as a single molecule.
- (General)
Specifies the force field for molecules other than proteins and water molecules. Internally, acpype is used for GAFF, GAFF2, OPLS/AA-L+GAFF, an in-house program for Dreiding, a proprietary extension of OpenBabel for UFF, and mktop for OPLS-AA. The configuration for Dreiding is described in
polymer/dreiding.lib.txt. Check Universal Force Field for details on UFF.- Exception
Assigns a user-specified LJ parameter to a specific molecule, instead of using the force field selected in (General). Check the molecules for which you want to assign LJ parameters in the left column of the sub-window and enter the LJ parameters in the right column.
Note
This is used, for example, when you want to assign LJ parameters to atoms in the solid phase in a solid-liquid interface system.
- (Protein)
Specify the force field of the protein. Here, the atom to which the name of the amino acid residue is assigned in the PDB or gro format is recognized as a protein. Internally, gmx pdb2gmx is used.
Warning
This function is not available if the molecular structure is read from a file that does not contain residue names.
- (Water)
Specifies the force field of water molecules. You must specify the water model selected in Solvate/Build Cell. Internally, the parameters are taken from the library of Gromacs topologies installed in Cygwin.
- [position_restraints] added for proteins
If the protein is present, write information (in the
[position_restraints]section) to the topology file to constrain the position with -POSRES in the Advanced tab. If the protein is not present, it is ignored.- [position_restraints] added for selected atoms
Writes information (in the
[position_restraints]section) to the topology file for a user-specified molecule to constrain its position with -POSRES on the Advanced tab. This is used, for example, to constrain the solid phase in a solid-liquid interface system.- [distance/angle/dihedral_restraints] added for selected atoms
Writes information to the topology file to constrain the distance, angle, and dihedral angle with -POSRES on the Advanced tab for the molecule specified by the user.
- Dump Now
Generate a file with force fields assigned based on the current settings.
Note
If you want to customize the forcefield information by editing it with a text editor or similar, first save the file containing the forcefield information using Dump Now and edit the top for Gromacs or the data file for LAMMPS with a text editor or similar. Please use a text editor or similar to edit the data file.
Next, for Gromacs, import the gro file at (select Discard and Load), then at Assign Force Field select :guilabel:` Select Use parameters written in topology file and click the OK button. You will then be asked for the location of the top file, so open the top file you just saved and edited.
For LAMMPS, import the data file by (select Discard and Import), select Use parameters written in file in main window for Assign Force Field Use the parameters written in the file in the :guilabel:`main window and click on the Next > button.If the data file does not contain force field information, you will be prompted to Select the type of force field, select the type of generic force field you want to use and click the OK button.
Charges are taken from the structure displayed in the main window. If more than one type of charge is set in the main window (for example, if you open a GAMESS log file and set a Mulliken charge and a Lowdin charge), the (high priority) User charge > NBO charge > Lowdin charge > ESP charge > Mulliken charge (low priority) Priority is used in that order.
- Using parameter files (for inorganic, ReaxFF, and DPD)
(for LAMMPS) Select if you want to use the potential for inorganic materials, ReaxFF or DPD. After pressing the Next > button, specify the type of force field you actually want to use. pair_style and Potential file must be set in [Tools]-[Preferences]-[Calculations] to allow the user to enter them freely.
- Use parameters written in topology file
(For Gromacs) Select this option if you want to run MD calculations using a top file that already exists. The corresponding gro file must be opened or imported in the main window. If you edit the structure after opening or importing it, the correspondence with the top file will be broken and the calculation will not be possible. If you want to use this function after editing the structure after opening or importing it to the extent that it does not affect the force field information (for example, editing only the coordinates without changing the bonds), export the structure in gro format after editing it and open or import that file before using this function.
- Use parameters written in file in main window
(For LAMMPS) Select this option if you want to run the MD calculation using a data file that already exists. The main window must have the data file you want to use open or imported. If you edit the structure after opening or importing the file, the correspondence with the top file will be broken and the calculation will not be possible. After pressing the Next > button, specify the type of force field to use.
8.3.2. Workflow Configuration
Set up and run Towhee’s calculation flow in project mode.
- Preset
Recalls and saves a preset of settings.
- # of Jobs
Specifies the number of jobs.
- Enable parameter/structure scan
This feature requires the purchase of an add-on. It allows you to run multiple calculations where only certain parameters differ (parameter scan) or to run calculations with the same parameters for multiple structures (structure scan).
Click Config to open the configuration window for the scan calculation.For parameter scans, select %WM_SCAN1% for the Target Variable and enter the parameters you wish to set for %WM_SCAN1% in each row of the Values.Then, enter %WM_SCAN1% in the parameters you want to set in the Workflow Settings window or Keyword Settings window.For structure scan, select %WM_STRUCT% for Target Variable when the animation appears in the molecule display area (e.g., by opening an SDF file).
After the scan calculation is finished, use to tabulate the calculation results.
- Import
Load the settings output by Export. Click the arrow to the right of the button to recall settings used in the past on the same project or Winmostar.
- Export
Output settings to file.
- OK
Run a calculation or generate a file with your settings. See For project mode for details.
- Details
Set detailed calculation conditions. The Keyword Settings will be launched.
- Ensemble
Specifies the type of ensemble.
- Temperature
Specify temperature.
- Pressure
Specify pressure.
- # of steps
Specifies the number of steps to execute.
- # of snapshots
Specifies the number of steps to execute.
- Chemical Potential
Specify chemical potential.
- For equilibration
This is used for equilibration calculations, not for this calculation. It uses an algorithm that has no statistical validity but allows the system to relax quickly.
- Calc as Rigid
Forces the CBMC probability to be zero and computes the numerator as a rigid body. This improves calculation speed because the computation of internal degrees of freedom is omitted.
- Precision
Set calculation precision.
8.3.3. Keyword Settings
Set the Towhee calculation conditions. After setting, press the Run button to run the calculation immediately, or press the OK button to return to the main window once more.
:guilabel:See Run Towhee for behavior when Run is clicked.
If there are molecules with no charge assigned, Assign Charges Automatically will automatically start up. If no forcefield is assigned, Assigning force fields will automatically raise.
Reset button to return to the default state. The Save button saves your settings except for the Force Field. The Load button loads the settings saved at Save.
- Continue Simulation
Running continuation job.
See Run Towhee for details.
- Preset
Specify presets for calculation conditions. Each preset changes the following keywords:
ensemble
nvt
nvt
npt
npt
Ratio(Vol)
0
0
0.001
0.001
Ratio(Insert)
0
0
0
0
rmin
0.01
1.0
0.01
1.0
Specify nstep/maxdispfreq
False
True
False
True
ensemble
uvt
uvt
Ratio(Vol)
0
0
Ratio(Insert)
0.001
0.001
rmin
0.01
1.0
Specify nstep/maxdispfreq
False
True
ensemble
nvt
nvt
npt
npt
Ratio(Vol)
0.001
0.001
0.001
0.001
Ratio(Insert)
0.001
0.001
0.001
0.001
rmin
0.01
1.0
0.01
1.0
Specify nstep/maxdispfreq
False
True
False
True
- Basic
- nstep
Specify the number of steps.
- ensemble
Specify ensemble.
- temperature
Specify temperature.
- pressure
Specify pressure.
- chempot
Specify chemical potential.
- random_seed
Specifies the seed of the random number.
- random_allow_restart
In continuation jobs, inherit the state of random number generation in the previous job.
- Specify ratio instead of cumulative probabilities
If checked, specifies the probability of each operation (translation, rotation, CBMC, volume, insertion). If unchecked, specifies the integration probability; CBMC is an update operation for intramolecular degrees of freedom.
- Disable CBMC
Forces CBMC probability to 0. All molecules are treated as rigid.
- Fix 1st component
Freeze the coordinates of the first molecular species that appears in the system (or the first molecular species that appears through the first or second system in the case of GEMC).
- Specify nstep/maxdispfreq
Give trmaxdispfreq and volmaxdispfreq as a ratio to nstep.
- trmaxdispfreq
Specify how often to automatically update the maximum displacement for translational and rotational operations.
- volmaxdispfreq
Specify how often to automatically update the maximum displacement for volume operations.
- Advanced (1)
- pmtracm
Specifies the cumulative probabilities of translational operations; if Specify ratio instead of cumulative probabilities is checked, you cannot enter the value directly and the automatically calculated value will be displayed.
- pmtcmt
Specifies the cumulative probability for each molecular species of a translational operation; if there are more than two molecular species, enter them separated by spaces.
- rmtrac
Specifies the maximum displacement for translational operations.
- tatrac
Specify the target adoption rate to update with trmaxdispfreq.
- pmrotate
Specify cumulative probabilities for rotational operations.If Specify ratio instead of cumulative probabilities is checked, you cannot enter the value directly and the automatically calculated value will be displayed.
- pmromt
Specifies the cumulative probability for each molecular species of the rotation operation.If there are more than two types of molecules, enter them separated by spaces.
- rmrot
Specifies the maximum displacement for rotational operations.
- tarot
Specify the target adoption rate to update with trmaxdispfreq.
- pmcb
Specify cumulative probabilities for CBMC operations; CBMC is an intramolecular degree of freedom update operation.If Specify ratio instead of cumulative probabilities is checked, you cannot enter it directly and the value will be calculated automatically.
- pmcbmt
Specifies the cumulative probability for each molecular species in a CBMC operation.If there are more than two types of molecules, enter them separated by spaces.
- pmall
Specify the probability for each molecular species that the entire molecule will be regenerated in a molecular regenerating operation.If there are more than two types of molecules, enter them separated by spaces.
- pmvol
Specify cumulative probabilities for volume operations.If Specify ratio instead of cumulative probabilities is checked, you cannot enter the value directly and the automatically calculated value will be displayed.
- pmvlpr
Enter the total probability of volume operation for each phase, separated by spaces if there are more than two phases.
- rmvol
Specifies the maximum displacement for volume operations.
- tavol
Specifies the target adoption rate to update with volmaxdispfreq.
- Advanced (2)
- pmuvtcbswap
Specify cumulative probabilities for insert and delete operations in GCMC. If Specify ratio instead of cumulative probabilities is checked, you cannot enter the value directly and the automatically calculated value will be displayed.
- pmuvtcbmt
Specify the cumulative probability for each molecular species for insert and delete operations in GCMC. If there are more than two types of molecules, enter them separated by spaces.
- pm2boxrbswap
Specify the cumulative probabilities of rigid insertion operations in GEMC. If Specify ratio instead of cumulative probabilities is checked, you cannot enter the value directly and the automatically calculated value will be displayed.
- pm2rbswmt
Specifies the cumulative probability for each molecular species of a rigid insertion operation in GEMC. If there are more than two types of molecules, enter them separated by spaces.
- pm2rbswpr
Specifies the integration probability for each interphase of a rigid insertion operation in GEMC. If there are more than three phases of molecules, enter them separated by spaces.
- pm2boxcbswap
Specify cumulative probabilities for flexible insertion operations in GEMC
- pm2cbswmt
Specifies the cumulative probability for each molecular species of a flexible insertion operation in GEMC
- pm2cbswpr
Specifies the integration probability for each interphase of a flexible insertion operation in GEMC. If there are more than three phases of molecules, enter them separated by spaces.
- Output
- printfreq
Specify how often statistics should be output on standard output.
- moviefreq
Specify how often to output trajectory files.
- blocksize
Specifies the size of the block when block averaging.
- backupfreq
Specify how often to output the restart file.
- restartfreq
Specify how often to output a restart file with the number of steps in the name.
- pdb_output_freq
Specify how often to output PDB files.
- pressure_virial_freq
Specify how often to calculate virial pressure.
- chempotperstep
Specifies the number of times per MC step of additional insertion operations for chemical potential calculations.
- loutchempotdata
Specify whether chemical potentials should be output to another file.
- Interaction
- rcut
Specifies the cutoff radius of the vdw(LJ) potential.
- rmin
Specify a hard inner cutoff where no more atoms can approach. A reasonable value will speed up the calculation.
- rcutin
Specifies the inner cutoff used by CBMC.
- ltailc
Specifies whether the cutoff correction term for the vdw potential is present.
- electrostatic_form
Specify whether electrostatic potential calculations are performed.
- coulombstyle
Specifies how the electrostatic potential is calculated.
- kmax
Specifies the maximum wavenumber in the Ewald method.
- kalp
Specify the product of the alpha parameter of the Ewald method and the short side of the cell.
- rcelect
Specifies the real space cutoff radius for the Ewald method.
- ewald_prec
Specifies the relative precision of the Ewald method.
- Options
- Restore Working Folder
Click to restore the working folder to its pre-execution state, for example, when a continuation job terminates abnormally.
- Reset
Reset settings.
- Import
Loading configuration file.
- Export
Output configuration file.
8.3.4. Run Towhee
Runs Towhee. The method of execution depends on the situation.
- (Default) Continue Simulation is unchecked
Generate a new wmm file before starting the job.
- Continue Simulation is checked
Start a job using
towhee_finalin the working folder associated with the wmm file open in the main window.The following files will be generated upon execution. As an example, the file/folder name of the input file is
water.wmm. Note that thewmmfile is Winmostar’s proprietary molecular structure file and is not directly read by Towhee.
Type
Description.
water.batwater_twh_tmp\The following files are generated in the working folder. Only the major files are shown here.
Type
Description.
towhee_inputtowhee_fftowhee_coordstowhee_initialtowhee_finalof the previous job at the time of the continuation job.lammps_datatowhee_coords,towhee_ff,towhee_input.gromacs.toplammps_dataand topology file for Gromacs with equivalent conditions. Can be used for result analysis.towhee.logtowhee_movietowhee_finalHint
**Working Folder**
A working folder is a folder whose name is the name of the file opened in the main window plus a suffix.
**Suffixes vary depending on the type of solver. **
For example, in Gromacs, if the file open in the main window is
aaa.growith the suffix_gmx_tmp, the working folder is namedaaa_gmx_tmp.Must be placed in the same level as the file that is open in the main window.
Processing flows in the working folder of the same name even for continuation jobs, 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 lowest numbered to the extent that there are no duplicate names. For example, if your working folder is
aaa_gmx_tmp, it will beaaa_gmx_tmp1.**Unnumbered directories are always up-to-date. **
Job will be run with Winmostar Job Manager.
8.3.5. Show log
Open the Towhee log file (
towhee.log) in a text editor.
8.3.6. Displays excerpts of key information from the log file.
Displays excerpts of key information from the log file.
8.3.7. Animation
towhee_inputandtowhee_movieto animate the trajectory of the MC calculation.See Animation operation area for animation display controls.
8.3.8. Energy Change
Select
towhee.logto display graphs of various thermodynamic quantities such as energy, temperature, and pressure.See Energy Plot window for subwindow operation.