amber_protocols

• amber_protocols
  • Resources
  • Example workflow
    • Run replicas
      • Restart individual replicas
  • Utils
    • loop_step: prmtop inpcrd step nrep basename
    • run_steps: prmtop inpcrd protdir protglob basename"
    • rep_step: step rep

Repository of computational biochemistry protocols for the Amber package

Set up AMBERPROTOCOLS environment variable for ease of use

export AMBERPROTOCOLS=<path-to-this-repo>

Resources

• AmberTools
• Amber22 Reference Manual
• Tutorials
• AmberHub

Example workflow

1. Copy the desired protocol folder to your working directory

cp -r $AMBERPROTOCOLS/protocols/protein/protocol protocol

2. (optional) If needed, edit the protocol files

3. Edit the loader script with the appropriate atom selection masks for your system. Note, the & character must be escaped, e.g.: & → \&

4. Run load.sh to load the protocol and the run.sh template in your working directory. This also loads the loop_step and run_steps runner scripts.

./protocol/load.sh

5. Edit the run.sh script with the appropriate parameters for your system:

RUN_EQUIL=true               # Whether to run the equilibration steps
NAME=MD_equil                # The basename for MD files
PRMTOP=system.prmtop         # Input topology
INPCRD=system.inpcrd         # Input coordinates
PROTDIR=.                    # Directory containing protocol *.in files
PROTGLOB='*.in'              # Glob pattern matching MD input files (mdin)

...

RUN_PROD=false               # Whether to run the production MD
NAME=MD_prod                 # The basename for MD files
INPCRD=last_step.rst7        # The input coordinates for the production run (usually the rst7 from the last equilibration step)
STEP_IN=Prod.mdin            # The name of the production step
NSTEPS=10                    # The number of times to repeat the production step

6. Run the simulation

sbatch run.sh

Run replicas

5. Edit the run.sh script with the appropriate parameters for your system: use the $REPLICA_DIR env variable to specify paths relative to each replica.

RUN_EQUIL=true               # Whether to run the equilibration steps
NAME=$REPLICA_DIR/MD_equil                # The basename for MD files
PRMTOP=system.prmtop         # Input topology
INPCRD=system.inpcrd         # Input coordinates
PROTDIR=.                    # Directory containing protocol *.in files
PROTGLOB='*.in'              # Glob pattern matching MD input files (mdin)

...

RUN_PROD=false               # Whether to run the production MD
NAME=$REPLICA_DIR/MD_prod                 # The basename for MD files
INPCRD=$REPLICA_DIR/last_step.rst7        # The input coordinates for the production run (usually the rst7 from the last equilibration step)
STEP_IN=Prod.mdin            # The name of the production step
NSTEPS=10                    # The number of times to repeat the production step

6. Edit the run_replica.sh script

NREPLICAS=6           # Number of replicas
BASENAME=replica      # Basename of replica directory

7. Run the simulations in parallel

./run_replica.sh

Restart individual replicas

# re-launch job for replica_3
env REPLICA_DIR=replica_3 sbatch run.sh

Utils

loop_step: prmtop inpcrd step nrep basename

Repeat a step (mdin) nrep times, with the output of each run being used as the input for the next one.

run_steps: prmtop inpcrd protdir protglob basename"

Launch a series of steps (mdin) in sequence, with the output of each step being used as the input for the next one. Step configurations are searched for in protdir directory, sorting any file matching the protglob pattern.

rep_step: step rep

Copy a configuration (mdin) file rep times, adding a progressive suffix. Useful to repeat the same step multiple times using run_steps.