This tutorial assumes basic GNU/Linux knowledge, a successful
installation of RUMD and a little portion of gumption mixed
with interest in molecular dynamics. For plotting the results
from simulations it is assumed that xmgrace is installed, but
other plotting programs can be used if you prefer.
The basic work-flow of doing simulations is:
The following sub-sections will take you through these steps.
- Specify initial condition, i.e., the initial positions
and velocities to be used in the simulation. This also involves
the number of particles () and the (initial) density
- Running the actual simulation. This can be done interactively
or by a script in python. It includes defining how particles
interact with each other (i.e., the potentials used), what
integrator to use (and the associated parameters, e.g.,
time-step and temperature.)
- Post-processing data analysis.