6.13. MD ‣ LAMMPS menu

It is a menu related to LAMMPS.

6.13.1. How to set up LAMMPS

To install LAMMPS, install CygwinWM version 2023/04/05 or later, which contains /opt_win/LAMMPS*/bin/ in lmp_serial.exe and lmp _mpi.exe and so on.

The configuration for using LAMMPS from Winmostar is done at Tools ‣ Preferences menu. If you have newly installed Winmostar V11.5.0 or later and are using CygwinWM 2023/04/05 version or later, no configuration is required.

First, select the LAMMPS lmp_serial.exe, lmp_mpi.exe or lmp.exe to use with program path ‣ LAMMPS. (When you select lmp_serial.exe to run MPI, the lmp_mpi.exe in the same folder is automatically used.) Next, under Calculation ‣ mpiexec (LAMMPS), select MPICH or Select and choose the MPI mpiexec.exe you want to use. If you want to use LAMMPS stored in CygwinWM, select /opt_win/MSMPI/Bin/mpiexec.exe under CygwinWM. Finally, at Calculation ‣ Options for mpiexec (LAMMPS), enter the arguments for mpiexec.exe. If you use LAMMPS in CygwinWM, enter -np %WM_ NUM_PROC%.

If you want to add a potential file, click Tools ‣ Preferences menu ‣ Calculation ‣ MD ‣ LAMMPS potential folder ‣ Open potential directory and in the opened folder Add potential files to the opened folder.

How to install LAMMPS on a remote machine is described in Installing Winmostar and solvers.

6.13.2. Assign Force Field

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

In the case of LAMMPS, if a gro file containing velocities is open in the main window at the time this function is used, a data file containing velocities is generated. Similarly, in the case of Gromacs, if a data file with velocities is open, a gro file with velocities is generated; this is useful when you want to take over Gromacs and LAMMPS calculation 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.

Automatically assign parameters

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

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)

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 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. If the force field information is not written in the data file, you will get a Choose the type of force field, choose 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 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 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 opened on 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.

6.13.3. Workflow Setup

Set up and run the LAMMPS calculation flow in project mode. 12-Step Compression in Preset is the polymer equilibration procedure described in [Hofmann2000] , [Larsen2011] . Also, 21-Step Compression-Decompression is the polymer equilibration procedure described in [Larsen2011].

[Hofmann2000]

4. Hofmann, L. Fritz, J. Ulbrich, C. Schepers and M. Bohning, Macromol. Theory Simul., 9 (6), (2000), 293–327.

[Larsen2011] (1,2)

G.S. Larsen, P. Lin, K.E. Hart and C.M. Colina, Macromolecules, 44 (17), (2011 ), 6944-6951.

Preset

Import and saves a preset of settings.

# of Jobs

Specify the number of jobs.

Enable parameter/structure scan

This feature requires the purchase of an add-on. It is possible to run multiple calculations in which 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 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 the structure scan, select %WM_STRUCT% for the Target Variable with the animation appearing in the molecule display area (e.g., by opening an SDF file).

After the scan calculation is finished, use File ‣ Project ‣ Scan Results to tabulate the calculation results.

Import

Import the settings output by Export. Click the arrow at 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 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
NPT(z)	Ensemble=npt Pressure control=z
NVE	Ensemble=nve
NPH	Ensemble=nph
NPH(z)	Ensemble=nph Pressure control=z
NPT+Rescale Cell	Ensemble=npt Rescale cell size=True
NVE+Rescale Vel	Ensemble=NVE Rescale velocities=True
NVT(DPD)	Ensemble=nve
NVT(SLLOD)	Ensemble=nvt Reset COM=Disable Enable SLLOD=True

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
High	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

6.13.4. 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.

Use berendsen thermostat

Use fix temp/berendsen instead of fix nvt or npt to control temperature.

Use velocity rescaling

Use fix temp/rescaling instead of fix nvt or npt 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.

Use berendsen barostat

Use fix press/berendsen instead of fix nph or npt to control pressure.

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.

Velocity rescaling interval

Specify how often to apply speed scaling.

Velocity rescaling window

Specify the window (allowable range from set temperature) when applying speed scaling.

Velocity rescaling fraction

Specifies the fraction at which to apply speed scaling; if 1.0, it will match the set temperature immediately after application.

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.

Dump Interval (restart)

Specify how often to output the restart file, in number of time steps.

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).

Flush log

Flush each time when the log is output.

Include velocities in dump custom

When outputting in dump format, also output the velocity.

Calculate Fluctuation Properties

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

Calculate Thermal Conductivity

Calculate and output the thermal conductivity on-the-fly from the autocorrelation function of the atomic flow velocity and the Green-Kubo equation. This method uses the fix ave/correlate command, so the length of the autocorrelation function is fixed.

Calc interval

Specifies how often the autocorrelation function is calculated.

ACF length

Specifies the length of the autocorrelation function. The maximum time for an autocorrelation function is (Calc Interval)×(ACF Length)×(Time Step).

Calculate viscosity

Calculates and outputs viscosity on-the-fly from the autocorrelation function of the pressure tensor and the Green-Kubo equation. This method uses the fix ave/correlate command, so the length of the autocorrelation function is fixed.

Calc interval

Specifies how often the autocorrelation function is calculated.

ACF length

Specifies the length of the autocorrelation function. The maximum time for an autocorrelation function is (Calc Interval)×(ACF Length)×(Time Step).

Calculate heat flux relaxation

Output autocorrelation functions for atomic heat flow. This method uses the fix ave/correlate/long command (multiple-tau correlator), so you can automatically get long-time autocorrelation functions depending on the simulation time. Thermal conductivity can be calculated separately from post-processing.

Calc interval

Specifies how often the autocorrelation function is calculated.

Dump Interval

Specifies the output frequency of the autocorrelation function.

Calculate stress relaxation

Output autocorrelation function for the pressure tensor. This method uses the fix ave/correlate/long command (multiple-tau correlator) so you can automatically get long autocorrelation functions depending on simulation time. Viscosity can be calculated separately from post-processing.

Calc interval

Specifies how often the autocorrelation function is calculated.

Dump Interval

Specifies the output frequency of the autocorrelation function.

Calculate dipole relaxation

Outputs the autocorrelation function of the dipole moments for the entire system. This method uses the fix ave/correlate/long command (multiple-tau correlator) so you can automatically get long-time autocorrelation functions depending on simulation time.

Calc interval

Specifies how often the autocorrelation function is calculated.

Dump Interval

Specifies the output frequency of the autocorrelation function.

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.

Non-equiliibrium (2)

Enable adding force

Target atoms applies a force in the z-direction to the atoms specified in Target atoms. The force applied is the value of Target Pzz and the area of the XY plane of the simulation cell. In solid-liquid interfacial systems, this is useful when you want to apply a force to a solid (slab) and adjust the pressure throughout the system.

Target atoms

Press the Select Group button with the atoms you want to force registered beforehand with Select Registered Group and select that group.

Target Pzz

Enable adding force

Enable direct density control

Force the simulation cell to be linearly deformed so that the density is at the value of Density at final step at the final step. The deformation is analogous. This is useful when the pressure control is not stable but you want to compress the system to some extent.

Density at final step

:guilabel:Specifies the density of the final step in the Enable direct density control feature.

Enable SLLOD method

Enable SLLOD method calculation.

Shear strain rate

Specifies the shear rate for SLLOD method calculations.

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.

Additional Commands

Add any command just before the read_data line, just before the run (or minimize) line, and just after the run (or minimize) line.

Manual entry

The contents of the generated LAMMPS input script (in file) will be displayed. You can also edit directly at this location. Any additional information you add here will be discarded when you edit other keywords. If you want to avoid this, fill in the Additional Commands field.

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.

6.13.5. 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.data	It is the initial state file of the calculation specified by read_data.
lmp.in	It is a file that specifies calculation conditions.
lmp.log	It is a log file. It is the same as: file: water.log.
lmp.dump	It is a trajectory file in dump format.
lmp.restart	It is a restart file containing information on the final state.
lmp_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.xtc	Trajectory file in xtc format for using the Gromacs tool for results processing.
lmp.gro	gro-format coordinate file to use the Gromacs tool for processing results. Convert from the data file specified as the input file
lmp.top	:guilabel:Specifies the density of the final step in the Enable direct density control feature. 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.

6.13.6. Open Log File

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

6.13.7. Show log excerpts

Displays excerpts of key information from the log file.

6.13.8. 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 operation area.

In the case of calculations where changes in chemical bonds occur, such as ReaxFF, checking the Options ‣ Enable Dynamics Bond checkbox in the Animation Manipulation Area will determine whether or not a bond exists based on the bond distance at each step, allowing you to see how the bond changes. You can check how the bond changes.

6.13.9. 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.

6.13.10. 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.

6.13.11. Analyses

6.13.11.1. 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.

6.13.11.2. 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.

6.13.11.3. 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.

6.13.11.4. 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.

6.13.11.5. 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.

6.13.11.6. 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.

6.13.11.7. Various autocorrelation functions (ave/correlate)

Displays the autocorrelation function created by the fix ave/correlate command, which is output when calculating thermal conductivity and viscosity using the Green-Kubo formula

6.13.11.8. Various autocorrelation functions (ave/correlate/long)

Displays the autocorrelation function created by the fix ave/correlate/long command.

6.13.11.9. 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.

6.13.11.10. 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.

6.13.11.11. radius of inertia

Select the xtc file output by LAMMPS and the gro, ndx, mdp, top files automatically generated by Winmostar, and analyze the radius of inertia of the selected group. mdp and top files can only be generated when using a general purpose force field such as GAFF, so this function is not available when using parameter files. This function cannot be used when parameter files are used.

See Radius of Gyration for details.

6.13.11.12. Atom/Group Distance Change

Select the xtc file output by LAMMPS and the gro, ndx, mdp, top files automatically generated by Winmostar to analyze the change in distance between specific atoms or groups of atoms. 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 Atom/Group Distance Change for details.

6.13.11.13. viscosity

The viscosity is calculated from the stress autocorrelation function obtained with the Multiple tau correlator (fix ave/correlate/long). The upper graph shows the normalized autocorrelation function C(t)/C(0) in a log-linear plot, the middle graph shows it in a log-log plot, and the lower graph shows the viscosity obtained from the integrated autocorrelation function. The autocorrelation function plot shows the function fitted to the lower equation in green.

In the lower graph, the short-time side has a large error due to insufficient integration range, while the long-time side has a large error due to insufficient sampling of the autocorrelation function.

Also, the time (excluding the short-time oscillation component) that the fitted function is below the value entered for Threshold for switching integration from raw to fitted is displayed in the Switch integration at. The Estimated Viscosity displays the viscosity obtained by integrating the autocorrelation function with the trapezoidal formula. The numerical integration is performed over the Switch integration at time, with the short integration over the autocorrelation function obtained directly from the calculation and the long integration over the function fitted to the above equation. Integrating the long time side over the function fitted to the above equation reduces the effect of errors due to under-sampling.

6.13.11.14. Thermal Conductivity

Calculate thermal conductivity from the autocorrelation function of the heat flow obtained with the multiple tau correlator (fix ave/correlate/long). The upper graph shows the normalized autocorrelation function C(t)/C(0) in a log-log plot, the middle graph shows a log-log plot, and the lower graph shows the thermal conductivity obtained from the integrated value of the autocorrelation function. The autocorrelation function plot shows the function fitted to the lower equation in green.

In the lower graph, the short-time side has a large error due to insufficient integration range, while the long-time side has a large error due to insufficient sampling of the autocorrelation function.

Also, the time (excluding the short-time oscillation component) that the fitted function is below the value entered for Threshold for switching integration from raw to fitted is displayed in the Switch integration at. The Estimated Viscosity displays the thermal conductivity obtained by integrating the autocorrelation function with the trapezoidal formula. The numerical integration is performed over the Switch integration at time, where the short time side is integrated over the autocorrelation function directly obtained from the calculation, and the long time side is integrated over the function fitted to the above equation. Integrating the long time side over the function fitted to the above equation reduces the effect of errors due to under-sampling.

6.13.12. Dissipative Particle Dynamics

6.13.12.1. 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.

6.13.12.2. 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).

Gamma

Enter the coefficient of friction (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.