6.13. MD ‣ LAMMPS menu

It is a menu related to LAMMPS.

The method of installing LAMMPS is described in Installing Winmostar and solvers.

6.13.1. Assign Force Field

Set the force field. The choices vary depending on the type of solver.

Automatically assign parameters

Assign a new force field parameter.

(General)

Specify the force field for molecules other than proteins and water molecules. In the case of GAFF, GAFF2 or OPLS/AA-L+GAFF, acpype is used, in the case of Dreiding, an in-house program is used, and in the case of UFF, a program that extends OpenBabel is used. The setting of Dreiding is written in polymer/dreiding.lib.txt. See Universal Force Field for more information about UFF.

Exception

For specific molecules, assign the user specified LJ parameters without using the force field selected in (General). In the left column of the subwindow, check the molecule you want to specify the LJ parameter and enter the LJ parameter in the right column.

Note

For example, when you want to allocate LJ parameters to solid phase atoms in a solid-liquid interface system.

(Protein/Ion)

Specify the force field of the protein. At this point, atoms assigned amino acid residue names in PDB and gro format are recognized as proteins. Internally gmx pdb2gmx is used. CygwinWM $GMXDATA/top/amber03.ff/ions.itp is used to determine if it is an ion residue name.

Warning

This function can not be used when reading the molecular structure from a file not including residue name.

(Water)

Specify the force field of the water molecule. You must specify the selected water model with Solvate/Build Cell. Internally we get the parameters from the library of Gromacs topology installed in Cygwin.

Add [position_restraints] for protein

If a protein exists, write information ([position_restraints] section) to constrain the position in the topology file with -POSRES on the Advanced tab. Ignored when protein is absent.

Add [position_restraints] for selected atoms

For the molecule specified by the user, write information ([position_restraints] section) to constrain the position in the topology file with -POSRES on the Advanced tab. For example, when fixing solid phase in solid-liquid interface system.

Add [distance/angle/dihedral_restraints] for selected atoms

For the molecule specified by the user, write information to constrain distance, angle, dihedral angle to topology file by -POSRES on the Advanced tab.

Dump Now

Based on the current settings, generate a topology file.

Note

  • If you want to customize the forcefield information by editing it with a text editor, 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.

  • Next, for Gromacs, import the gro file at File ‣ Import File (select Discard and import), 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 at File ‣ Import File (select Discard and import), then at Assign Force Field, select Use the parameters written in file opened on :guilabel:`main window and click on the Next > button. Then, Select force field appears. Select the general type of force field 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 the GAMESS log file is opened and Mulliken charge and Lowdin charge are set), the following order of priority is used: (high priority) User charge > NBO charge > Lowdin charge > ESP charge > Mulliken charge (low priority). When the file is opened and the Mulliken charge and Lowdin charge are set (for example, when the file is opened and the Mulliken charge and Lowdin charge are set), the order of priority is User charge > NBO charge > Lowdin charge > ESP charge > Mulliken charge (low priority).

Use parameters defined in external parameter file (for inorganic system, ReaxFF or DPD)

(For LAMMPS) Select when you want to use inorganic potential, ReaxFF or DPD. After pressing Next > button, specify the type of force field to be actually used.

Use parameters written in topology file

(For Gromacs) Select to perform MD calculation using the existing top file. The corresponding gro file must be open in the main window.

Use parameters written in file opened on main window

(For LAMMPS) Select to execute MD calculation using the existing data file. The data file to be used must be open in the main window. After pressing Next > button, specify the type of force field to use.

6.13.2. Workflow Setup

Set up and run the LAMMPS calculation flow in project mode.

Preset

Import and saves a preset of settings.

# of Jobs

Specify the number of jobs.

Import

Import the settings output by Export. Click the arrow to the right of the button to recall settings used in the past.

Export

Output settings to file.

OK

Run a calculation or generate a file with your settings.

Details

Set detailed calculation conditions. The Configure will be launched.

Ensemble

Specifies the type of ensemble.


Setting details
Minimize
Ensemble=minimize
NVT
Ensemble=nvt
NPT
Ensemble=npt
NPT(aniso)
Ensemble=npt
Pressure control=aniso
NVE
Ensemble=nve
NPH
Ensemble=nph
NPT+Rescale Cell
Ensemble=npt
Rescale cell size=True
NVE+Rescale Vel
Ensemble=NVE
Rescale velocities=True
NVT(DPD)
Ensemble=nve
Temperature

Specify the temperature.

Pressure

Specify the target pressure.

Simulation time

Specify simulation time.

# of snapshots

Specify number of dump and xtc outputs.

Initial velocity

If Random, the first speed is generated randomly; if From parent, the last speed of the previous job is inherited.

Free boundary condition

Calculate with free boundaries instead of periodic boundary conditions.


Setting details
True
Boundary=fff
Neighbor search=nsq
Reset COM motion=angular
False
Boundary=ppp
Neighbor search=bin
Reset COM motion=linear
Precision

Set calculation precision.


Setting details
Low
Cutoff(vdW)=10
Cutoff(Coulomb)=10
Log interval=10
Time step(fs)=2
Tchain=3
Pchain=3
Shake tolerance=1e-5
PPPM order=4
K-space accuracy=1-e5
Medium
Cutoff(vdW)=12
Cutoff(Coulomb)=12
Log interval=20
Time step(fs)=1
Tchain=3
Pchain=3
Shake tolerance=1e-6
PPPM order=4
K-space accuracy=1e-6
Low
Cutoff(vdW)=15
Cutoff(Coulomb)=15
Log interval=40
Time step(fs)=0.5
Tchain=1
Pchain=1
Shake tolerance=1e-9
PPPM order=6
K-space accuracy=1e-9

6.13.3. Configure

Set calculation condition of LAMMPS. To set up the calculations immediately after setting Run button, once to return to the main window please press OK button.

Behavior when clicking Run is see Run.

Assign Charges Automatically will be launched automatically if there is a molecule to which no charge is assigned. If no force field is assigned, Assign Force Field will be launched automatically.

Return to the default state with Reset button. Save the setting except Force Field with Save button. Load the setting saved by Save with the Load button.

Continue Simulation

Execute a continuous job.

For details, see Run.

Preset

Specify the preset of the calculation condition. Each preset changes the following keywords.

Minimize
(fast)
NVT
(fast)
NPT
(fast)
NVE
(fast)

Pair style

lj/cut/coul/long

lj/cut/coul/long

lj/cut/coul/long

lj/cut/coul/long

Time step

2.0

2.0

2.0

# of time steps

5000

5000

5000

5000

Ensemble

minimize

nvt

npt

nve

Generate
initial velocity

True

False

False

Temperature

300

300

Pressure

1.0

Boundary Condition

p p p

p p p

p p p

p p p

Reset COM motion

linear

linear

linear

linear

Tchain

3

3

Pchain

3

Shake tolerance

1e-5

1e-5

1e-5

Dump interval
(dump)

100

100

100

100

Dump interval
(xtc)

100

100

100

100

Log interval

10

10

10

10

Cutoff (vdW)

Cutoff (Coulomb)

PPPM order

4

4

4

4

K-space accuracy

1e-5

1e-5

1e-5

1e-5

Minimize
(medium)
NVT
(medium)
NPT
(medium)
NVE
(medium)

Pair style

lj/cut/coul/long

lj/cut/coul/long

lj/cut/coul/long

lj/cut/coul/long

Time step

1.0

1.0

1.0

# of time steps

10000

10000

10000

10000

Ensemble

minimize

nvt

npt

nve

Generate
initial velocity

True

False

False

Temperature

300

300

Pressure

1.0

Boundary Condition

p p p

p p p

p p p

p p p

Reset COM motion

linear

linear

linear

linear

Tchain

3

3

Pchain

3

Shake tolerance

1e-6

1e-6

1e-6

Dump interval
(dump)

200

200

200

200

Dump interval
(xtc)

200

200

200

200

Log interval

20

20

20

20

Cutoff (vdW)

Cutoff (Coulomb)

PPPM order

4

4

4

4

K-space accuracy

1e-6

1e-6

1e-6

1e-6

Minimize
NVT
NPT
NVE

Pair style

lj/cut/coul/long

lj/cut/coul/long

lj/cut/coul/long

lj/cut/coul/long

Time step

0.5

0.5

0.5

# of time steps

20000

20000

20000

20000

Ensemble

minimize

nvt

npt

nve

Generate
initial velocity

True

False

False

Temperature

300

300

Pressure

1.0

Boundary Condition

p p p

p p p

p p p

p p p

Reset COM motion

linear

linear

linear

linear

Tchain

1

1

Pchain

1

Shake tolerance

1e-9

1e-9

1e-9

Dump interval
(dump)

400

400

400

400

Dump interval
(xtc)

400

400

400

400

Log interval

40

40

40

40

Cutoff (vdW)

Cutoff (Coulomb)

PPPM order

K-space accuracy

Minimize
(vapor,fast)
NVT
(vapor,fast)
NPT
(vapor,fast)
NVE
(vapor,fast)

Pair style

lj/cut/coul/cut

lj/cut/coul/cut

lj/cut/coul/cut

lj/cut/coul/cut

Time step

2.0

2.0

2.0

# of time steps

5000

5000

5000

5000

Ensemble

minimize

nvt

npt

nve

Generate
initial velocity

True

False

False

Temperature

300

300

Pressure

1.0

Boundary Condition

f f f

f f f

f f f

f f f

Reset COM motion

angular

angular

angular

angular

Tchain

3

3

Pchain

3

Shake tolerance

1e-5

1e-5

1e-5

Dump interval
(dump)

100

100

100

100

Dump interval
(xtc)

100

100

100

100

Log interval

10

10

10

10

Cutoff (vdW)

Cutoff (Coulomb)

PPPM order

K-space accuracy

Minimize
(vapor)
NVT
(vapor)
NPT
(vapor)
NVE
(vapor)

Pair style

lj/cut/coul/cut

lj/cut/coul/cut

lj/cut/coul/cut

lj/cut/coul/cut

Time step

0.5

0.5

0.5

# of time steps

20000

20000

20000

20000

Ensemble

minimize

nvt

npt

nve

Generate
initial velocity

True

False

False

Temperature

300

300

Pressure

1.0

Boundary Condition

f f f

f f f

f f f

f f f

Reset COM motion

angular

angular

angular

angular

Tchain

1

1

Pchain

1

Shake tolerance

1e-9

1e-9

1e-9

Dump interval
(dump)

400

400

400

400

Dump interval
(xtc)

400

400

400

400

Log interval

40

40

40

40

Cutoff (vdW)

Cutoff (Coulomb)

PPPM order

6

6

6

6

K-space accuracy

1e-9

1e-9

1e-9

1e-9

Minimize
(ReaxFF)
NVT
(ReaxFF)
NPT
(ReaxFF)
NVE
(ReaxFF)

Pair style

reax/c

reax/c

reax/c

reax/c

Time step

0.5

0.5

0.5

# of time steps

20000

20000

20000

20000

Ensemble

minimize

nvt

npt

nve

Generate
initial velocity

True

False

False

Temperature

300

300

Pressure

1.0

Boundary Condition

p p p

p p p

p p p

p p p

Reset COM motion

linear

linear

linear

linear

Tchain

1

1

Pchain

1

Shake tolerance

1e-9

1e-9

1e-9

Dump interval
(dump)

400

400

400

400

Dump interval
(xtc)

400

400

400

400

Log interval

40

40

40

40

Cutoff (vdW)

Cutoff (Coulomb)

PPPM order

K-space accuracy

MPI

Specify MPI parallel number.

Basic
Units

Specify the unit system.

real

It is mainly specified by molecular system (A, fs, Kcal/mol).

metal

It is mainly specified by crystal system (A, ps, eV).

lj

It is mainly specified by DPD calculation (dimensionless unit).

Atom Style

Specify the type of system to calculate. Units changes accordingly.

Pair Style

Select the method of interaction calculation.

Force Field/Potential File

If Units is real, specify the type of force field. Affects the special_bonds, bond_style, angle_style, dihedral_style, and improper_style keywords.

Select the potential file when Units is other than “real”. List the files in the Potential folder directly under the folder where you installed the LAMMPS main unit. The choices will change according to Pair Style.

Time Step

Specify the step size of time integration. Units are selected according to the selected Unit.

# of Time Steps

Specify the maximum number of time integration steps.

Ensemble

Specify the type of time integration. nvt (canonical ensemble with constant temperature), npt (temperature, constant pressure ensemble), nve (micro and canonical ensemble with constant volume and energy), minimize (CG Energy minimization by law).

Generate Velocity

If you check, the initial speed will be given.

Random Seed

Specify the seed of the pseudorandom number at the time of initial velocity occurrence.

Temperature

Specify the target temperature. At the time of annealing calculation, specify the temperature of the start condition.

Tdamp

Specify the time constant parameter for temperature control.

Pressure Control

Specify how cells are moved during pressure control.

Pressure

Specify the target pressure.

Pdamp

Specify the time constant parameter of pressure control.

Advanced
Boundary X Y Z

Specify the periodic boundary condition. p (periodic), f (non-periodic and fixed), s (non-periodic and shrink-wrapped), m (non-periodic and shrink-wrapped with a minimum value).

Energy Tolerance

minimize Specifies the truncation error on energy during calculation.

Force Tolerance

minimize Specifies the truncation error on force during calculation.

Reset COM Motion

Choose a method to freeze motion of the center of gravity of the whole system during MD calculation.

Reset Interval

Specify Reset COM Motion frequency in time step

Tchain

Specify the number of stages of Nose-Hoover chain.

Pchain

Specify the number of stages of pressure control.

Constrain hydrogen atoms

We restrict hydrogen atoms by SHAKE method.

SHAKE tolerance

Specify the truncation error of the SHAKE method.

Automatically disable Shake if CH4-like molecule exists

Automatically disables the SHAKE method when methane like molecules are included.

Set “box tilt large”

Specify the allowable degree of deformation of the simulation cell.

Output
Dump Interval (dump)

Specify the frequency of outputting coordinates in dump format as the number of time steps.

Dump Interval (xtc)

Specify the frequency of outputting coordinates in xtc format as the number of time steps.

Dump Interval (xyz)

Specify the frequency of outputting coordinates in xyz format by time step number.

Log Interval

Specify the frequency of writing energy variables to the log file by time step number.

Print log in high precision

Increases the number of digits of the energy variable to be written to the log file.

Sort dump file by id

Makes the order of particles in the dump file sorted by id (consecutive number).

Calculate Fluctuation Properties

Calculates and outputs on-the-fly specific heat and isothermal compression ratio from fluctuations of thermodynamic quantities.

Calculate Thermal Conductivity

Output thermal conductivity calculated from autocorrelation function of atomic flow velocity.

Calc Interval

Specify the calculation frequency of autocorrelation function in thermal conductivity calculation.

ACF Length

Specify the length of autocorrelation function in thermal conductivity calculation.

Calculate viscosity

Viscosity is calculated on-the-fly from the autocorrelation function of the pressure tensor and the Green-Kubo equation.

Calc Interval

Specify the calculation frequency of autocorrelation function in thermal conductivity calculation.

ACF Length

Specify the length of autocorrelation function in thermal conductivity calculation.

Interaction
Modify cutoff radii not to exceed L/2

If checked, Cutoff(vdw) and Cutoff(Coulomb) are automatically adjusted so that they do not exceed half the lattice constant.

Neighbor Search

Specify algorithm for near particle search.

Neighbor Skin

Specify the extra radius of the search radius when searching for nearby particles.

Cutoff(vdw)

vdw (LJ) Specifies the cutoff radius of the potential.

Enable Long Range Correction

Specify the presence or absence of the vdw potential cut-off correction term.

Cutoff(Coulomb)

Coulomb (electrostatic) Specify the cutoff radius of the potential.

Disable Ewald(PPPM) if no charge exists

Automatically disables the Ewald (PPPM) method when the system has no charge.

Automatically set Nmesh

The number of meshes of the PPPM method used when Pair Style = lj/cut/coul/long is automatically set from K-space accuracy.

Nmesh for kx, ky, kz

Specify the mesh number of PPPM method.

PPPM Order

Specify Spline interpolation order of PPPM method.

K-space accuracy

Specify the allowable relative error of PPPM method.

Non-equiliibrium (1)
Enable Elongation

Enable decompression calculation. Ensemble can be specified when it is not minimize.

Affine Transformation

Specify whether to modify the atom position according to the simulation cell and to affine (similarity) deformation during elongation calculation.

Eng. Strain Rate

Specify the extension speed at extension calculation with industrial strain. Max Eng. Strain shows the predicted value of the strain at the final step.

Preserve Volume

During elongation calculation, deform the cell size in the direction perpendicular to the elongation direction so that the volume of the simulation cell is kept constant.

Enable Pulling

Enable Pull calculation to move a specified atom group at a constant speed. Ensemble can be specified when it is not minimize.

Pulled Atoms

Press Select Group button and select the group in the state where the atoms you want to pull are registered by Select Registered Group in advance.

Pull Velocity

Specify the pull speed for Pull calculation.

Enable Simulated Annealing

Enable annealing calculations (calculation to change the temperature at a constant speed). Ensemble can be specified when nvt, npt. The value of Temperature is the temperature at the beginning, and the value of Final Temperature is the temperature of the final state.

Final Temperature

Specify the temperature of the final state at the time of annealing calculation.

Annealing Rate

The heating or cooling rate at the time of annealing calculation is displayed.

Enable pressurization

Enable annealing calculations (calculation to change the temperature at a constant speed). Ensemble can be specified when nvt, npt. The value of Temperature is the temperature at the beginning, and the value of Final Temperature is the temperature of the final state.

Final Pressure

Specify the temperature of the final state at the time of annealing calculation.

Enable electric field

Gives an external electric field. If you select Sine wave, the electric field is given sine wave. When Constant is selected, the electric field is given in static.

Amp & Freq

Gives the intensity (Amp) and frequency (Freq) of each direction. If Sine wave in Enable electric field is selected, the following formula is used to give the electric field, where A is the intensity and f is the frequency. If you choose Constant, only the intensity is used.

A \sin ( 2 \pi f t)

Restraint
Enable Restraint

Calculation is performed by constraining the distance between specified two atoms. Ensemble can be specified when it is not minimize.

Restrained Atoms

When you click the Set button, the two atoms with the markers become the target of the constraint.

Bond Length

Specify the constraint distance between two atoms at the time of constraint calculation.

Initial Strength

Specify the spring coefficient of the constraint potential in the starting state at the time of constraint calculation.

Final Strength

Specify the spring coefficient of the constraint potential in the final state at the time of constraint calculation.

Enable Position Restraint

Calculate with the absolute coordinates of the specified atom fixed. The temperature of the unfixed atom is output to the log as TempFree.

Restrained Atoms

Press Select Group button to select the group with the atoms to be constrained registered with Select Registered Group in advance, .

Use spring potential

If Restrained Atoms is checked, the atoms will be restrained by the spring potential from their initial position. If Reset positions of restrained atoms after run is checked, the atoms will be returned to their initial positions after the calculation is finished, so they will not move away from their initial positions even if you repeat the continue simulation. If the Restrained positions of atoms after run checkbox is checked, the position will be returned to the initial position after the calculation.

Spring constant

Specify the spring coefficient when using the spring potential.

Reset positions of restrained atoms after run

When using the spring potential, the position of the constrained atoms is reset to the initial position after the calculation is complete.

Automatic
Rescale velocities to..

Use it when you want to bring the system temperature closer to the target temperature in the NVE ensemble. Calculate the scaling factor from the average temperature under calculation and the temperature entered here and scale the velocity of each particle in the final structure.

Rescale cell size to..

It is used when calculating with the NVE or NVT ensemble in the state close to the set pressure after calculating with the NPT ensemble. Scale the final structure to the average cell size under calculation.

Manual entry

The contents of the generated LAMMPS input script (in file) are displayed. You can also edit directly at this location.

Options
Restore Working Folder

Click this button to return the working folder to the state before execution, such as when the continued job terminates abnormally.

Dump all files for remote

Output files necessary for job execution under Linux environment. The same file as the file generated by Remote job function is output.

Generate gro & ndx files every time

If it is not checked, gro and ndx files will not be generated for continuous jobs.

Reset

Reset settings.

Import

Loading configuration file.

Export

Output configuration file.

6.13.4. Run

Execute LAMMPS. The execution method differs depending on the situation.

  • (Default) Continue Simulation is unchecked and Automatically assign parameters or Use parameters defined in external parameter file (for inorganic system, ReaxFF or DPD) in Assign Force Field is selected

    Create a new data file (file containing coordinates and topology) and start the job.

  • Continue Simulation is unchecked and Use parameters written in file opened on main window” in Assign Force Field is selected

    Start the job using the data file opened in the main window.

  • When Continue Simulation is checked

    Start the job using the lmp_tmp_final.data located in the working folder associated with the data file opened in the main window.

Following file will be generated with execution. As an example, the file/folder name when the input file is water.data is also shown.

type

Description

out file
water.log

This is the log file of LAMMPS.

bat file
water.bat
LAMMPS and its pre/post processing
Working Folder
water_lmp_tmp\
Working folder.

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

type

Description

lmp_tmp.data
It is the initial state file of the calculation specified by read_data.
lmp_tmp.in
It is a file that specifies calculation conditions.
lmp_tmp.log
It is a log file.
It is the same as: file: water.log.
lmp_tmp.dump
It is a trajectory file in dump format.
lmp_tmp.restart
It is a restart file containing information on the final state.
lmp_tmp_final.data
It is a data file containing information on the final state.
It is generated from the restart file.
postproc.sh
The lmp_tmp_final.data generated by LAMMPS is not sufficient to run LAMMPS as is, so this script does some processing to make up for the insufficient information.
lmp_tmp.xtc
Trajectory file in xtc format for using the Gromacs tool for results processing.
lmp_tmp.xtc
Trajectory file in xtc format for using the Gromacs tool for results processing.
lmp_tmp.gro
gro-format coordinate file to use the Gromacs tool for processing results.
Convert from the data file specified as the input file

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.

    • The suffix varies depending on the type of solver.

    • For example, in the case of Gromacs, if the file opened in the main window is: file: aaa.gro and the suffix is _ gmx_tmp, the working folder will be named aaa_gmx_tmp .

  • It must be in the same hierarchy as the file opened in the main window.

  • Processing continues in the working folder of the same name even when continuing jobs, but by default the backup of the working directory of the previous job is created just before the continuation job is executed.

    • The name of the backup will be the one with the smallest number in the range where duplicate names do not exist. For example, if the working folder is aaa_gmx_tmp, it is aaa_gmx_tmp1.

    • Directories without numbers are always up to date.

The job is run through Winmostar Job Manager.

6.13.5. Open Log File

Open the LAMMPS log file ( *.log ) with a text editor.

6.13.6. Show log excerpts

Displays excerpts of key information from the log file.

6.13.7. Animation

Select the data file and dump file and animate the MD calculation trajectory.

The file name of the main window does not change.

For the animation display operation method, see Animation display area.

6.13.8. Energy Plot

Select the log file and display a graph of various thermodynamic quantities such as energy, temperature and pressure. You can plot the value specified by thermo_style.

Please see Energy Plot window for how to operate subwindow.

6.13.9. Import Last Coordinate (data)

Open *_lmp_tmp\lmp_tmp_final.gro.

When using this function, the file name of the main window does not change.

6.13.10. Analyses

6.13.10.1. Radial Distribution Function

Select the xtc file output by LAMMPS and the gro, ndx file automatically generated by Winmostar and display the radial distribution function.

See Radial Distribution Function for details.

6.13.10.2. Diffusion Constant/Mean Square Displacement

Select the xtc file output by LAMMPS and the gro, ndx file automatically generated by Winmostar, and display the mean square displacement and the self diffusion coefficient.

See Diffusion Constant/Mean Square Displacement for details.

6.13.10.3. Scattering Function

Select the xtc file output by LAMMPS and the gro, ndx file automatically generated by Winmostar and display the scattering function.

For details, see Scattering Function.

6.13.10.4. Static Dielectric Moment

Select the xtc file output by LAMMPS and the gro, ndx file automatically generated by Winmostar and display the scattering function.

See Radial Distribution Function for details.

6.13.10.5. Density Profile

Select the xtc file output by LAMMPS and the gro, ndx file automatically generated by Winmostar and display the radial distribution function. Since mdp and top files can only be generated when using general-purpose force fields such as GAFF, this function cannot be used when using parameter files.

See Radial Distribution Function for details.

6.13.10.6. Free Volume

Select the xtc file output by LAMMPS and the gro, ndx, mdp and top files automatically generated by Winmostar and display the free volume. Since mdp and top files can only be generated when using general-purpose force fields such as GAFF, this function cannot be used when using parameter files.

See Free Volume for details.

6.13.10.7. Autocorrelation Function

Displays the autocorrelation function that is output when calculating the thermal conductivity and viscosity using the Green-Kubo equation.

6.13.10.8. Bond/Angle/Dihedral Distribution

Select the xtc file output by LAMMPS and the gro, ndx file automatically generated by Winmostar and display the radial distribution function. Since mdp and top files can only be generated when using general-purpose force fields such as GAFF, this function cannot be used when using parameter files.

For details, see Scattering Function.

6.13.10.9. Hydrogen bonding analyses

Select the xtc file output by LAMMPS and the gro, ndx, mdp, top files automatically generated by Winmostar and analyze the hydrogen bonds between the selected groups. mdp and top files can only be generated when using generic forcefields such as GAFF. This function is not available when using parameter files.

See Radial Distribution Function for details.

6.13.11. Dissipative Particle Dynamics

6.13.11.1. DPD Cell Builder

Create a simulation cell for dissipative particle dynamics.

Reset

Restore all settings to default.

Monomers Available

Select the monomer (particle) that constitutes the polymer chain.

>> Add >>

Add selected monomers.

<< Delete <<

Delete the added monomer.

Branch
Start

Specify the branch start position.

End

Specify the branch end position.

Monomers Used

A list of added monomer species and number is displayed.

Clear

Delete all listed monomer species.

>> Add >>

Add the listed polymer chain to the calculation target.

<< Delete <<

Delete the added polymer chain.

Export

Output the contents of Monomer Used to a file.

Import

Reads the contents of Monomer Used from a file.

Polymers Used

The composition and number of added polymer chains are listed.

Build

Enter dimensionless densities and build simulation cells.

Close

Close the window.

6.13.11.2. DPD Potential Editor

Winmostar Create and edit a potential file for proprietary dissipative particle dynamics.

Potential Files

Select the potential file used for dissipative particle dynamics.

New

We will create a new potential file.

Delete

Delete the selected potential file.

Mass tab
Species

The name of the monomer (particle) is displayed.

Mass

Set the mass (dimensionless).

Bond tab
R_0

Set bond (bond) potential parameter R_0 (equilibrium distance, dimensionless).

TO

Set bond (bond) potential parameter K (spring constant, dimensionless).

Nonbond tab
Aij

Enter the unbonded potential parameter Aij (dimensionless).

Rcut

Enter the unbonded potential parameter Rcut (cutoff radius, dimensionless).

Set

The set potential parameters are reflected in the list.

OK

Save the set potential parameters in the potential file and close the window.

Close

Discard the settings and close the window.