MD Engines

Below are all currently supported engines to generate shooting points with.

Available Engines:

• CP2K
• GROMACS
• Implementing a New Engine

Warning

Constant pressure (changing box sizes) is not currently supported

Intro to Engines

All engines share some common features that need to be specified in the inputs. In particular, these are

engine - the engine name

String defined by the engine implementation of the method get_engine_str()

Example:

• "engine": "cp2k" - use the cp2k engine implementation

md_cmd - the command line command to invoke the engine

The string you would use to run the MD engine from the command line normally, leading up to the path of the engine executable. Any additional commands (such as mpirun) can be prepended, but the final argument should be the engine executable.

Warning

You should not rely on relative paths of executables. They should either be in the PATH environment variable when invoked, or the full path should be given.

Examples of valid commands:

• "md_cmd": "/path/to/cp2k/exec" - just use the standard cp2k executable.

• "md_cmd": "mpirun -n 2 -genv 1 /path/to/cp2k/exec" - Run cp2k with MPI with two processes

  Note

  Since the aimless shooting algorithm runs the forwards and backwards trajectories in parallel, the ideal number of MPI processes is equal to num_cores/2, so cores are distributed evenly across the two trajectories.

Examples of invalid commands:

• "md_cmd": "/path/to/cp2k/exec -i my_input_file -o my_output_file" - arguments after the engine executable should be left to the module

plumed_file - the path to the PLUMED file with the committor basins for the system

The plumed file that defines the basins associated with a complete reaction. This should stop the system when the simulation commits to a basin (NOSTOP=off, the default) and the output file name should not be defined (FILE not specified). See COMMITOR for more details.

Suppose we had a system with two atoms. The following PLUMED would consider the ending reaction states to be when the atoms were closer than 0.15nm or further than 1nm apart:

d1:  DISTANCE ATOMS=1,2
COMMITTOR ...
  ARG=d1
  BASIN_LL1=0
  BASIN_UL1=.15
  BASIN_LL2=1
  BASIN_UL2=100
... COMMITTOR

Note

Take care that PLUMED has its atoms indexed starting at 1.

An equivalent plumed file with the COMMITTOR on one line could also be used:

d1:  DISTANCE ATOMS=1,2
COMMITTOR ARG=d1 BASIN_LL1=0 BASIN_UL1=.15 BASIN_LL2=1 BASIN_UL2=100