MD Simulations

class MD([theory=None, driver='namd', ...])

MD simulations can be carried out using the MD() driver, which expects a Theory object and a driver option, e.g.

my_theory = NAMD(...)
my_job = MD(theory=my_theory, driver='namd', ...)

Though MD() is a general-purpose driver, we currently only support classical MDs with the NAMD molecular dynamics simulation package. Please read:

For ChemShell’s basic MD analysis tool please see: MD analysis.

Methods

MD.run(dryrun=False, info_filename='_profile_md.npz')
Parameters

  • dryrun (bool, optional) – If the function is called with dryrun=True, the job will only generate input scripts without executing real calculatons

  • info_filename (str, optional) – Filename for writing out compressed trajectory profile data for plotting purpose. Please see: how to plot trajectories

The MD simulation is run with this method, for example:

my_job.run()