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.

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 File ‣ Import File (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 File ‣ Import File (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 inorganic potentials, ReaxFF or DPD. After pressing the Next > button, specify the type of force field you actually want to use.

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 File ‣ Project ‣ Scan Results Viewer 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.

	Configuration
NVT	ensemble=nvt Ratio(Vol)=0 Ratio(Insert)=0
NPT	ensemble=npt Ratio(Vol)=0.001 Ratio(Insert)=0
uVT	ensemble=uvt Ratio(Vol)=0 Ratio(Insert)=0.001
GEMC-NVT	ensemble=nvt Ratio(Vol)=0.001 Ratio(Insert)=0.001
GEMC-NPT	ensemble=npt Ratio(Vol)=0.001 Ratio(Insert)=0.001

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.

	Configuration
True	rmin=0.01 Specify nstep/maxdispfreq=False
False	rmin=1.0 Specify nstep/maxdispfreq=True

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.

	Configuration
Low	rcut=8 ewald_prec=1d-4
Medium	rcut=10 ewald_prec=1d-5
High	rcut=12 ewald_prec=1d-6

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:

	NVT Equil	NVT Prod	NPT Equil	NPT Prod
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

	uVT Equil	uVT Prod
ensemble	uvt	uvt
Ratio(Vol)	0	0
Ratio(Insert)	0.001	0.001
rmin	0.01	1.0
Specify nstep/maxdispfreq	False	True

	GEMC-NVT Equil	GEMC-NVT Prod	GEMC-NPT Equil	GEMC-NPT Prod
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_final in 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 the wmm file is Winmostar’s proprietary molecular structure file and is not directly read by Towhee.

Type	Description.
bat file water.bat	This is a a batch file for running Towhee and its pre- and post-processing.
Workign folder water_twh_tmp\	Working folder

The following files are generated in the working folder. Only the major files are shown here.

Type	Description.
towhee_input	This is the main input file with some of the calculation conditions and force field information.
towhee_ff	This file contains force field parameters and other information.
towhee_coords	File with initial coordinates.
towhee_initial	This is the towhee_final of the previous job at the time of the continuation job.
lammps_data	Coordinates and force field files for LAMMPS used to generate towhee_coords , towhee_ff , towhee_input.
gromacs.top	lammps_data and topology file for Gromacs with equivalent conditions. Can be used for result analysis.
towhee.log	Towhee’s standard output (log file).
towhee_movie	Trajectory file generated by Towhee calculations.
towhee_final	This file contains the final state at the end of the calculation (coordinates, various parameters of the Monte Carlo method, etc.).

Hint

**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.gro with the suffix _gmx_tmp, the working folder is named aaa_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 be aaa_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_input and towhee_movie to animate the trajectory of the MC calculation.

See Animation operation area for animation display controls.

8.3.8. Energy Change

Select towhee.log to display graphs of various thermodynamic quantities such as energy, temperature, and pressure.

See Energy Plot window for subwindow operation.