This protocol allows running classical molecular dynamics on any potential provided by cuby interfaces. Verlet propagator is used and several thermostats are available. It is possible to run the MD only on a part of the system, keeping the rest frozen.
The following examples, along with all other files needed to run them, can be found in the directory cuby4/protocols/dynamics/examples
#=============================================================================== # Molecular dynamics example 1 - setting temperatures #=============================================================================== # 1 ps of MD simulation (the default step is 1 fs) job: dynamics maxcycles: 1000 # Amber calculation of ace-ala-nme tripeptide from database interface: amber geometry: ace-xxx-nme:ala # Initial temperature - used only to generate the velocities at the start # of the simulation # Because we start from optimized structure, this temperature is set to # twice the desired temperature (100K) - the kinetic energy quickly equalizes # with potential energy. If we started from a MD snapshot where we already # have the potential energy, this will be set to teh actual temperature # we want, it is 100 K. init_temp: 200 # Thermostat thermostat: berendsen thermostat_tc: 0.1 # faster coupling needed for such a short simulation # This is the temperature maintained by the thermostat temperature: 100 # Optionally, the thermostated temperature can vary during the simulation. # Uncomment the following keyword to perform a simulation where the system is # gradually heated to 300 K over the course of the simulation. temperature_target: 300
#=============================================================================== # Molecular dynamics example 2 - restarting the simulation #=============================================================================== # This example demonstrates restarting a MD run job: multistep steps: first, second calculation_first: job: dynamics maxcycles: 100 # Amber calculation of ace-ala-nme tripeptide from database interface: amber geometry: ace-xxx-nme:ala # By default, the simulation starts with random velocities generated from # the Boltzmann distribution init_temp: 600 # Every MD run produces file 'last.xyz' containing the final geometry and # velocities. Alternatively (e.g. if the run did not finish), a snapshot from # the trajectory can be used instead trajectory_file: trajectory1.xyz calculation_second: # The same setup as in previous step job: dynamics maxcycles: 100 interface: amber # Geometry for amber must be read from a PDB file, we can't use last.xyz directly # Therefore, we load the original geometry and update coordinates from the # restart file. geometry: ace-xxx-nme:ala geometry_update_coordinates: last.xyz # Velocities are read from the restart as well: velocities: read velocities_file: last.xyz # Write to second trajectory file trajectory_file: trajectory2.xyz # The two trajectories produced should be equivalent to running a single, # longer MD simulation