md

An mdtask performs a NAMD simulation on the current state files; for example, those produced by the immediately previous psfgen task.

In most cases, it is only necessary to specify which ensemble (minimize, NVT, NPT, or NPAT) you want to run in, and how many MD steps:

tasks:
  - ... (prior tasks here)
  - md:
      ensemble: NVT
      nsteps: 1000
  - ... (subsequent tasks here)

The above md directive will run an NVT MD simulation at the default temperature of 300 K for 1000 time-steps. By default, any ensemble in which temperature is controlled will use a Langevin thermostat with a damping coefficient of 5/ps. The default NPT and NPAT ensembles use a Langevin piston barostat with a target pressure of 1 atm and a piston period of 100 fs. NPAT ensembles further restrict the ratio of the x and y dimensions of the box to maintain a constant ratio, which is useful for membrane simulations.

Default NAMD config file values can be overwritten in the top-level namd directive of the pestifer config file. The thermostat parameters can be overridden by specifying thermostat parameters, and the barostat parameters can be overridden by specifying barostat parameters. The NPAT parameters can be overridden by specifying membrane parameters.

A typical sequence of tasks for a new build might be a fetch task, then a psfgen task, followed by an md task to perform a vacuum energy minimization, followed then by a short md task to thermalize the protein:

tasks:
  - fetch:
      sourceID: 6pti
  - psfgen:
  - md:
      ensemble: minimize
  - md:
      ensemble: NVT

If you are using GPU-resident namd3, I recommend setting the cpu-override flag to True in any md task run in vacuum.