Command line tool: simplemd

Module	cltools
Description	Input
run lj code	file

Details

simplemd allows one to do molecular dynamics on systems of Lennard-Jones atoms.

You can use simplemd to do a molecular dynamics simulation on a system of Lennard-Jones particles by using the following command

plumed simplemdrun lj code More details < in This is the input file for the calculation.
The simplemd action with label plumed calculates something

The input to simplemd is specified in an input file that contains one directive per line like the one shown below.

#TOOL=simplemdrun lj code This action has hidden defaults. More details
inputfileAn xyz file containing the initial configuration of the system input.xyz
outputfileAn output xyz file containing the final configuration of the system output.xyz
temperature the temperature at which you wish to run the simulation in LJ units 0.722
tstep the integration timestep in LJ units 0.005
friction The friction (in LJ units) for the Langevin thermostat that is used to keep the temperature constant 1
forcecutoff  2.5
listcutoff   3.0
nstepThe number of steps of dynamics you want to run 50
nconfig The frequency with which to write configurations to the trajectory file followed by the name of the trajectory file 10 trajectory.xyz
nstat The frequency with which to write the statistics to the statistics file followed by the name of the statistics file   10 energies.dat

#TOOL=The simplemd action with label  calculates somethingsimplemdrun lj code This action uses the defaults shown here. More details
inputfileAn xyz file containing the initial configuration of the system input.xyz
outputfileAn output xyz file containing the final configuration of the system output.xyz
temperature the temperature at which you wish to run the simulation in LJ units 0.722
tstep the integration timestep in LJ units 0.005
friction The friction (in LJ units) for the Langevin thermostat that is used to keep the temperature constant 1
forcecutoff  2.5
listcutoff   3.0
nstepThe number of steps of dynamics you want to run 50
nconfig The frequency with which to write configurations to the trajectory file followed by the name of the trajectory file 10 trajectory.xyz
nstat The frequency with which to write the statistics to the statistics file followed by the name of the statistics file   10 energies.dat

epsilon LJ parameter 1.0
sigma LJ parameter 1.0
idum The random number seed 0
ndim The dimensionality of the system (some interesting LJ clusters are two dimensional) 3
wrapatoms If true, atomic coordinates are written wrapped in minimal cell false 

This input instructs simplemd to do 50 steps of MD at a temperature of 0.722 Lennard Jones Units. Notice that the atomic configurations are input and output in xyz format.

If you run the following command a description of all the directives that can be used in the input file will be output.

plumed simplemdrun lj code More details --help print this help
The simplemd action with label plumed calculates something

Syntax

The following table describes the keywords that should be used in the input file for this command line tool

Keyword	Description
--help/-h	print this help
nstep	The number of steps of dynamics you want to run
temperature	the temperature at which you wish to run the simulation in LJ units
friction	The friction (in LJ units) for the Langevin thermostat that is used to keep the temperature constant
tstep	the integration timestep in LJ units
epsilon	LJ parameter
sigma	LJ parameter
inputfile	An xyz file containing the initial configuration of the system
forcecutoff
listcutoff
outputfile	An output xyz file containing the final configuration of the system
nconfig	The frequency with which to write configurations to the trajectory file followed by the name of the trajectory file
nstat	The frequency with which to write the statistics to the statistics file followed by the name of the statistics file
idum	The random number seed
ndim	The dimensionality of the system (some interesting LJ clusters are two dimensional)
wrapatoms	If true, atomic coordinates are written wrapped in minimal cell