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PRISM Documentation

Custom Configurations

Custom Configuration Example¶

Quick Start

prism --export-config my_config.yaml
prism protein.pdb ligand.mol2 -o output --config my_config.yaml

Advanced system setup using YAML configuration files for fine-grained control over all PRISM parameters.

Overview¶

Learn how to: - Create and customize YAML configuration files - Control all aspects of system building - Set advanced MD parameters - Use configuration templates

Complexity: Advanced
Prerequisites: Completed Simple Example

Configuration File Structure¶

Complete Configuration Template¶

# PRISM Configuration File
# All parameters with defaults shown

general:
  overwrite: false
  verbose: true

# Force fields
forcefields:
  protein: amber99sb
  ligand: gaff
  water: tip3p

# Box configuration
box:
  distance: 1.5  # nm from protein to box edge
  shape: cubic   # cubic, dodecahedron, octahedron
  center: true

# Solvation and ions
ions:
  neutral: true
  concentration: 0.15  # M
  positive_ion: NA
  negative_ion: CL

# Simulation parameters
simulation:
  temperature: 310  # K
  pressure: 1.0     # bar
  pH: 7.4
  ligand_charge: 0
  production_time_ns: 500
  dt: 0.002  # ps
  equilibration_nvt_time_ps: 500
  equilibration_npt_time_ps: 500

# Protein preparation
protein_preparation:
  ion_handling_mode: smart  # smart, keep_all, remove_all
  metal_distance_cutoff: 5.0
  keep_crystal_water: false
  remove_crystallization_artifacts: true

# Output options
output:
  trajectory_interval_ps: 500
  energy_interval_ps: 10
  compressed_trajectory: true

# Constraints
constraints:
  algorithm: lincs
  type: h-bonds

Example Configurations¶

1. High-Accuracy Configuration¶

# config_accurate.yaml
forcefields:
  protein: amber14sb
  ligand: openff
  water: tip4p

box:
  distance: 2.0
  shape: dodecahedron

simulation:
  temperature: 300
  production_time_ns: 1000
  dt: 0.001  # Smaller timestep
  equilibration_nvt_time_ps: 1000
  equilibration_npt_time_ps: 1000

output:
  trajectory_interval_ps: 100  # More frequent output

2. Fast Screening Configuration¶

# config_fast.yaml
box:
  distance: 1.0  # Minimal box
  shape: cubic

simulation:
  production_time_ns: 50
  equilibration_nvt_time_ps: 250
  equilibration_npt_time_ps: 250

output:
  trajectory_interval_ps: 1000
  compressed_trajectory: true

3. Membrane Protein Configuration¶

# config_membrane.yaml
forcefields:
  protein: charmm36
  ligand: cgenff
  water: tips3p

simulation:
  temperature: 310
  pressure: 1.0

# No box for membrane (use pre-built membrane system)

Usage¶

import prism

# Use custom configuration
system = prism.system(
    "protein.pdb",
    "ligand.mol2",
    output_dir="custom_system",
    config="config_accurate.yaml"
)

system.build()

Advanced Features¶

Dynamic Parameter Overrides¶

# Start with config file, override specific parameters
system = prism.system(
    "protein.pdb",
    "ligand.mol2",
    config="config_accurate.yaml",
    production_ns=2000,  # Override config value
    temperature=320      # Override config value
)

Configuration Validation¶

from prism.utils.config import ConfigurationManager

config = ConfigurationManager("my_config.yaml")
config.validate()  # Check for errors
config.show()      # Display all settings

Best Practices¶

Start with Template: Export default config and modify
Version Control: Keep configs in git
Document Changes: Add comments to explain non-standard settings
Validate: Test configs on small systems first

What's Next¶