Developers.Variables.dynamics

Variable "dynamics" in MolDynSim

This variable specifies details of the molecular dynamics (trajectory) simulations in our mol_Dynamics.m and/or mol_MonteCarlo.m MATLAB function. It is a structured variable that should initially containing the following fields :

field	description
md.handle	choose propagator for positions/velocities (MATLAB function handle). See here for a list of available propagators/integrators
n_step	number of steps to be simulated (positive integer)
n_save	number of steps between saves (positive integer); use this to limit the size of the resulting trajectory files
t_step	size of time step (positive real number, in ps units, MD only)
seed	seed generation of random numbers; used for initial velocities (integer); use this to create reproducible sequences of random numbers
ensemble	choose thermodynamic ensemble, e. g., 'NVE', 'NVT' (three letter code). Not required for MonteCarlo which does NVT always.

Molecular dynamics NVE simulations only

field	description
e_total	desired value of total energy, achieved by scaling of initial velocities (real number in kJ/mol units) should be above global minimum of force field :-)
perturb	random perturbation of initial coordinates (real number in nm units)

Molecular dynamics NVT simulations only

field	description
tmp.handle	choice of "thermostat" algorithm (Matlab function handle). See here for a list of available thermostats
temperature	desired value of temperature (real positive number in Kelvin units); is achieved by using a "thermostat".

Monte Carlo NVT simulations only

field	description
mc.handle	variants of Monte Carlo algorithm (Matlab function handle). See here for a list of available random walkers
temperature	desired value of temperature (real positive number in Kelvin units); governs acceptance/rejection of steps in random walk
mc.delta	max. size of steps in random walk