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Advanced Usage

Table of Contents

  1. Introduction
  2. Customizing Simulation Settings
  3. Customizing Analysis Settings

Introduction

This document explains the detailed configuration options for EXPRORER_MSMD. Please refer to this after understanding Basic Usage when you want to have finer control over simulations and analyses.

Customizing Simulation Settings

We provide options to control simulation behavior in detail.

Controlling Simulation Steps

Options are available to execute each processing phase individually. This is useful when you want to reanalyze with different parameters or try analysis with different conditions.

# Skip preprocessing
# - When using an existing system
# - When system construction is complete but simulation needs to be rerun
./exprorer_msmd protocol.yaml --skip-preprocess

# Skip simulation
# - When performing different analyses on existing trajectories
# - When reanalyzing with modified analysis parameters
./exprorer_msmd protocol.yaml --skip-simulation

# Skip postprocessing
# - When only running simulations
# - When analysis will be performed separately
./exprorer_msmd protocol.yaml --skip-postprocess

Independent Trial Settings

You can run multiple independent simulations to increase reliability.

general:
  iter_index: 0,1,2  # Execute 3 independent trials
  # Notation:
  # "1-3" => 1,2,3
  # "5-9:2" => 5,7,9
  # "1-3,5-9:2" => 1,2,3,5,7,9

Adjusting Simulation Parameters

You can set parameters to control the physical conditions of the simulation.

exprorer_msmd:
  general:
    dt: 0.002          # Time step (ps)
    temperature: 300   # Temperature (K)
    pressure: 1.0      # Pressure (bar)
    pbc: xyz          # Periodic boundary conditions

  sequence:
    - name: pr        # Production run
      type: production
      nsteps: 20000000  # Number of steps (40 ns in this example)
      nstxtcout: 5000   # Output frequency (every 10 ps in this example)

Customizing Analysis Settings

We provide options to control how simulation results are analyzed.

PMAP Calculation Settings

You can control the calculation method of Probability MAP (PMAP) in detail.

map:
  type: pmap
  snapshot: 2001-4001:1  # Snapshot range to use: use data after equilibration
  maps:
    - suffix: nVH        # Map using heavy atoms only
      selector: (!@VIS)&(!@H*)
    - suffix: nV         # Map using all atoms
      selector: (!@VIS)
  map_size: 80           # Map size (Å): specify a size large enough to contain the entire system
  normalization: total   # Normalization method: total, snapshot, or GFE can be specified

Inverse MSMD Related Settings

You can configure settings for probe molecule environment analysis.

probe_profile:
  resenv:
    map: nVH            # Map to use: typically use heavy-atoms-only map
    threshold: 0.001    # Probability threshold: lower values detect wider range of interactions
  profile:
    types:
      - name: anion     # Interaction with anionic residues
        atoms:          # Specify atoms for interaction evaluation
          - ["ASP", " CB "]
          - ["GLU", " CB "]

For detailed explanations and recommended values for each setting, please also refer to example/example_protocol.yaml.