IMD

Parameters

IMD reads all simulation parameters from the parameter file, which is specified on the command line. In the case of a multiphase simulation, the parameter file contains the entire script describing the the simulation.

Each line in the parameter file contains one parameter, first its name, then its value (or values), separated by spaces or tabs. Empty lines are discarded, as is everything after a # character.

Certain parameters are required for every simulation, such as the simulation ensemble, the file with the starting configuration, the box size, the number of steps to be simulated, etc. IMD makes a rudimentary check whether every parameter needed is actually given.

Other parameters make sense only in a certain context. If a parameter appears in the parameter file, but is not needed in the current context, a warning is issued, and the parameter is ignored.

Valid Parameters

There is a list of all valid parameters, where each parameter is given with a short description of its meaning, and when it is needed. For the meaning of more specialized parameters, the description of the corresponding ensembles and options should be consulted.

Multiphase Simulations

An IMD simulation can consist of several phases. Many parameters, in particular the MD integrator to be used, can change from one phase to the next. Simulation phases are numbered consecutively, from 1 to N. The parameter file contains first the parameters for phase 1, then the parameters for phase 2, etc. The start of the parameter file section for phase n is announced with a line

simulation n

Announcing the parameters for the first phase is optional. Before phase n is started, the parameters of all phases up to n are (re-)read. If a certain parameter is not given afresh for the new phase, its value from the previous phase (or its default value) is retained. In other words, only paramters whose values have changed need be given for the later phases.

Certain parameters must not be changed during the simulation, like the box size. Also, it is probably a good idea to take care that the external temperature and pressure are continuous throughout the simulation. It is the user's responsibility that the parameter starttemp is equal to the parameter endtemp of the previous phase. A similar statement holds for the external pressure.

Example of a paramter file with 4 phases:

simulation      1     # this line is not really needed
ensemble        nvt   # nvt ensemble
maxsteps        1000  # phase stops at step 1000
starttemp       0.1   # starting temperature
endtemp         0.1   # ending temperature - temperature remains constant

other parameters for phase 1 (and the other phases)

simulation      2
maxsteps        2000  # phase stops at step 2000
starttemp       0.1   # not needed - does not change
endtemp         0.5   # ending temperature - temperature increases linearly

simulation      3
maxsteps        3000  # phase stops at step 3000
starttemp       0.5   # this IS needed - temperature should be continuous
endtemp         0.5   # not needed

simulation      4
maxsteps        4000  # phase stops at step 4000
ensemble	nve   # we continue with nve ensemble

All four phases last 1000 steps. The first three use the nvt ensemble, the last one the nve ensemble. In the second phase, the system is heated linearly from temperature 0.1 to temperature 0.5. Note that the parameter maxsteps is the step number at which the simulation phase ends, not the number of steps in the simulation phase.