NAMD using Turbomole¶
This section briefly describes how to run nonadiabatic molecular dynamics (NAMD) with mudslide using Turbomole as a QM engine.
Warning
This is a work in progress. Expect some kinks.
Setup Turbomole¶
The first step will be to setup a directory that contains all the input information you will need for a turbomole calculation. This means run define, TmoleX, or whatever else you would normally run to set up the calculation. Please see the Turbomole documentation for more information on how to do this. When the directory is set up, change to it:
cd /path/to/turbomole/directory
Load TMModel class¶
Next, you will set up a python script that will create a TMModel and run the simulation. An example script is shown below:
import mudslide
model = mudslide.models.TMModel(states=[0, 1]) # run using ground and first excited states
positions = model._position # read position from the coord file
momenta = mudslide.math.boltzmann_velocities(model._mass, 300) * model._mass
log = mudslide.YAMLTrace() # log trajectory using YAML files
traj = mudslide.TrajectoryCum(model, # run using turbomole model
positions, # start at position from coord
momenta, # use boltzmann momenta
1, # start on 1st excited state
tracer=log, # use yaml log
dt=20, # 20 a.u. time step
max_time=80, # run for 80 a.u.
)
results = traj.simulate()
Advice¶
Make sure your control file specifies all the options you need for dynamics. For example:
For NAMD you will need to have
$soes
data group with information on the excitations.$nacme
(for just states 0,1) or$nacme pseudo
(for state-to-state)weight derivatives
And it is recommended to have
$phaser
$do_etf