This is part of the cltools module

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

The input to simplemd is spcified in an input file. Configurations are input and output in xyz format. The input file should contain one directive per line. The directives available are as follows:

Compulsory keywords
nstep The number of steps of dynamics you want to run
temperature ( default=NVE ) the temperature at which you wish to run the simulation in LJ units
friction ( default=off ) The friction (in LJ units) for the langevin thermostat that is used to keep the temperature constant
tstep ( default=0.005 ) the integration timestep in LJ units
inputfile An xyz file containing the initial configuration of the system
forcecutoff ( default=2.5 )
listcutoff ( default=3.0 )
outputfile An output xyz file containing the final configuration of the system
nconfig ( default=10 ) The frequency with which to write configurations to the trajectory file followed by the name of the trajectory file
nstat ( default=1 ) The frequency with which to write the statistics to the statistics file followed by the name of the statistics file
maxneighbours ( default=10000 ) The maximum number of neighbours an atom can have
idum ( default=0 ) The random number seed
ndim ( default=3 ) The dimensionality of the system (some interesting LJ clusters are two dimensional)
wrapatoms ( default=false ) If true, atomic coordinates are written wrapped in minimal cell

You run an MD simulation using simplemd with the following command:

plumed simplemd < in

The following is an example of an input file for a simplemd calculation. This file instructs simplemd to do 50 steps of MD at a temperature of 0.722

temperature 0.722
tstep 0.005
friction 1
forcecutoff 2.5
listcutoff  3.0
nstep 50
nconfig 10
nstat   10 energies.dat

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

plumed simplemd --help