GROMACS Documentation

GROMACS Specific Inputs

In addition to the inputs required by all engines, the GROMACS specific inputs are listed below.

Template Input Files

These three files make up the base case simulation. None of the original files will be modified

mdp_file - path to the .mdp file to be used

The path to a well formed GROMACS .mdp file that specifies the simulation parameters. All existing parameters will be used, except:

  1. Any velocity generation - Aimless shooting will generate its own starting velocities

  2. The trajectory print frequency - This is modified for individual shootings to extract to relevant \(\Delta t\) positions

gro_file - path to a template .gro file to be used

The path to a corresponding .gro file. The coordinates and velocities of atoms do not need to reflect a transition state, this file is primarily used to define the atoms and their indices. Starting positions will be initialized from the start directory, and new velocities will be generated by aimless shooting.

top_file - path to a .top file corresponding to the system.

Nothing in this file will be modified.

Additional Commands

For md_cmd, you should include mdrun, e.g.:

  • "md_cmd": "gmx_mpi mdrun"

This should use the number of cores desired for one simulation. Each parallel simulation will be pinned to different cores (if enough are available) automatically by aimless shooting.

grompp_cmd - command to compile a simulation to a .tpr

This command will be used to compile a .mdp, a .gro, and a .top file into a .tpr before running a simulation, e.g.:

  • "grompp_cmd": "gmx_mpi grompp"

GROMACS Outputs

If GROMACS grompp or mdrun exits with a non-zero exit code, the output file is copied from the engine’s working directory with the name {projname}_FATAL.log, where projname is the root name of that shooting point. Additionally, all std out and std err is logged as a warning, with a note that this simulation failed. Note that this is not necessarily terminal, as multiple velocities are resampled. If many of these are occurring, something is likely wrong.

At this time, warnings are not checked in either grompp or mdrun’s output.

Additional Logging

Setting log_level = DEBUG will log the individual commands used for each grompp and mdrun so you can ensure they match your expectations.