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pyBrellaSampling

This is the readme for the pyBrellaSampling code.

The pyBrellaSampling code is primarily designed to assist in the setup and running of QM/MM Umbrella sampling using NAMD and ORCA. It is designed to work with initial AMBER coordinates and parameter files, however can be modified to use other files that are supported by NAMD. It is also designed to work both locally and using the SLURM work scheduler on an external HPC such as ARCHER2.

To work correctly, the user must have orca, namd and vmd available and in their path for the script to work.

Install pyBrellaSampling:

  1. Firstly clone this repo into a directory

    • gh repo clone pcyra2/pyBrellaSampling

  2. Copy files for pip outside of the Source directory

    • cp pyBrellaSampling/setup.py .

    • cp pyBrellaSampling/requirements.txt .

  3. Create an environment

    • conda create -n pyBrellaSampling --file requirements.txt -c conda-forge

    • conda activate pyBrellaSampling

  4. install the environment.

    • pip install -e .

Usage:

Umbrella Sampling:

To generate input files for umbrella sampling, run "pyBrella -jt inpfile", then edit all ".conf" files in order to set up your calculation, importantly:

  • "JobType" needs to be set to "umbrella"
  • "Stage" is the calculation stage, either "init", "min", "heat", "pull", "equil" or "prod"
  • "QmPath" is the full path location to your orca executable

WorkFlow:

  1. Setup input files (pyBrella -jt inpfile)
  2. Obtain a starting structure (--StartFile) and parameter file (called complex.parm7 and amber format)
  3. Perform a Minamization calculation (pyBrella -jt umbrella -stg min --StartFile STARTFILE -dr False)
  4. Heat the system (pyBrella -jt umbrella -stg heat -dr False)
  5. Check the current value of your reaction coordinate using vmd.
  6. perform initial pulls (On your fastest computer as this is not parallel.) (pyBrella -jt umbrella -stg pull -dr False)
  7. Setup your equil and prod files (pyBrella -jt umbrella -stg equil -dr True) (pyBrella -jt umbrella -stg prod -dr True)
  8. Copy all files to the server
  9. Submit the calculations using the runner.sh script. NOTE CARE MUST BE TAKEN WRT. THE SPECIFIC HPC SERVICE AS QUEUE LIMITS MAY BREAK THIS.
  10. Pull all results back
  11. Perform wham calculation (pyBrella -jt umbrella -stg convergence -dr False) If there are problematic undesirable reaction coordinates, add it to the BondErrors.dat or DihedralErrors.dat. This is experimental, however... good luck!

Standalone Calculations:

Although pyBrellaSampling was designed to run QM/MM Umbrella sampling simulations, it has the functionality to a variety of standalone calculations.

  • Molecular Dynamics
    • minimisation
    • heating
    • NVT
    • NPT
  • QM/MM
  • Steered/constrained molecular dynamics

It should be noted however that the initial code was NOT designed to do this and so may not work perfectly. It is recommended to thoroughly test the code in order to ensure that it works how you intend. If there are any issues, or you have any requests, please use the GitHub repo or email me on ross.amory98@gmail.com.

To generate input files for a standalone calculation, run "Standalone -jt inpfile", then edit all ".conf" files to suit your calculation.