.. _config_ref tasks md:

``md``
======

Parameters controlling a NAMD run

Single-valued attributes:

  * ``single-core``: whether or not to run namd on a single core; if false, namd3 will be used if available and appropriate for the system size (default: False)

  * ``cpu-override``: revert to cpu version of namd3 (default: False)

  * ``vacuum``: if true, namd will run on a single node even if multiple nodes are allocated (default: False)

  * ``ensemble``: Name of ensemble to run in; note that NPT can only be performed on a solvated system (default: NVT)

  * ``minimize``: Number of minimization steps; ignored if ensemble is not 'minimize' (used with the 'minimize' command) (default: 1000)

  * ``nsteps``: Number of MD time steps; ingored if ensemble is 'minimize' (used with the 'run' command) (default: 2000)

  * ``dcdfreq``: number of time steps between configuration output to DCD file (default: 100)

  * ``xstfreq``: number of time steps between cell size output to DCD file (default: 100)

  * ``temperature``: Temperature (K) for NVT or NPT (default: 300)

  * ``pressure``: Pressure (bar) for NPT; note that NPT can only be performed on a solvated system (default: 1)

  * ``other_parameters``: key:value pairs for other namd2 configuration file statements

  * ``colvar_specs``: colvar specifications; dict with keys 'groups', 'distances', and 'harmonics'



Container-like attribute:

.. toctree::
   :maxdepth: 1

   md/addl_paramfiles


Subattributes:

.. toctree::
   :maxdepth: 1

   md/constraints
   md/ssrestraints


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