6.12. MD ‣ LAMMPS menu

It is a menu related to LAMMPS.

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

6.12.1. 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 or OPLS/AA-L, 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.

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 edit the force field information with a text editor and customize it, first save this file using this function, and edit the top file for Gromacs and the data file for LAMMPS with a text editor etc. .
  • Next, in case of Gromacs, select Use parameters written in topology file and click OK button. Then you will be asked for the location of the top file, so open the top file you saved and edited earlier.
  • In case of LAMMPS, select Use parameters written in file in main window and click Next > button. Then, Select the type of force field appears. Select the general type of force field to use and click the OK button.
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.

6.12.2. 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.

Extending 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
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.
Calculate as rigid body
We treat molecules as rigid bodies.
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.
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.
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.
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, .
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 box 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
Make a Backup of Working Directory
Select this when backing up the working directory.
Restore Working Directory
Click this button to return the working directory 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.

6.12.3. Run

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

  • (Default) Extending 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.
  • Extending 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 Extending Simulation is checked
    Start the job using the lmp_tmp_final.data located in the working directory 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
It is a batch file.
Working Directory
water_lmp_tmp\
Working directory.

The following files are generated in the working directory. 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
lmp_tmp_final.data LAMMPS generated is
insufficient for the execution of LAMMPS,
It is a script that performs processing to compensate for insufficient information.
lmp_tmp.xtc
To use the Gromacs tool for processing results,
It is a trajectory file of xtc format.
lmp_tmp.xtc
To use the Gromacs tool for processing results,
It is a trajectory file of xtc format.
lmp_tmp.gro
To use the Gromacs tool for processing results,
It is a gro format coordinate file.
Convert from the data file specified as the input file
It will be created.

Hint

Working directory

  • A working directory 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 directory 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 directory 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 directory 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.

6.12.4. Open Log File

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

6.12.5. 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 window.

6.12.6. 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.

6.12.7. 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.

6.12.8. Analyses

6.12.8.1. 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.

6.12.8.2. 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.

6.12.8.3. 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.

6.12.8.4. 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.

6.12.8.5. Density Profile

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

See Radial Distribution Function for details.

6.12.8.6. 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.

See Free Volume for details.

6.12.8.7. Autocorrelation Function

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

6.12.8.8. 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.

For details, see Scattering Function.

6.12.9. Dissipative Particle Dynamics

6.12.9.1. DPD Cell Builder

Create a simulation cell for dissipative particle dynamics.

Monomers Available
Select the monomer (particle) that constitutes the polymer chain.
# of Monomers
Specify the number of selected monomers.
>> Add >>
Add selected monomers.
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.
<< Delete <<
Delete the added monomer.
# of Polymers
Specify the number of polymer chains.
>> Add >>
Add the listed polymer chain to the calculation target.
Polymers Used
The composition and number of added polymer chains are listed.
<< Delete <<
Delete the added polymer chain.
Density
Specify the density (dimensionless) of the system.
Build
Build a simulation cell.
Reset
Restore all settings to default.
Close
Close the window.

6.12.9.2. 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.