PLUMED Tutorial

Complete Guide from Installation to Molecular Dynamics Enhanced Sampling

Introduction

This tutorial will guide you through the installation, configuration, and basic usage of PLUMED. PLUMED is an open-source toolkit for molecular dynamics enhanced sampling, providing rich collective variables and enhanced sampling methods that can be integrated with various molecular dynamics software.

Installation Steps

1. System Requirements

  • Linux/Unix system
  • C++ compiler (GCC 4.8+)
  • CMake 3.0+
  • 4GB RAM (recommended 16GB+)

2. Download and Compile

# Download PLUMED
wget https://github.com/plumed/plumed2/releases/download/v2.8.0/plumed-2.8.0.tgz
tar -xzf plumed-2.8.0.tgz
cd plumed-2.8.0

# Configure and compile
./configure --prefix=/usr/local/plumed
make -j4
make install

3. Integrate with MD Software

# GROMACS integration example
source /usr/local/plumed/sourceme.sh
cd gromacs-2023.1
plumed patch -p
cmake .. -DGMX_MPI=ON -DGMX_GPU=ON
make -j4

Note: Ensure your system has installed the required dependencies such as MPI library and OpenMP.

Basic Usage

1. Prepare Input File

Create PLUMED input file (plumed.dat):

# Define collective variable
DISTANCE ATOMS=1,2 LABEL=d1

# Set metadynamics
METAD ARG=d1 SIGMA=0.1 HEIGHT=1.0 PACE=500 LABEL=metad

# Output file
PRINT ARG=d1,metad.bias FILE=COLVAR STRIDE=100

2. Run Simulation

# Use GROMACS to run
gmx mdrun -s topol.tpr -plumed plumed.dat

# Use AMBER to run
pmemd.cuda -O -i md.in -p prmtop -c inpcrd -o md.out -r restrt -x mdcrd -plumed plumed.dat

3. Analyze Results

Use PLUMED tools to analyze results:

# Calculate free energy
plumed sum_hills --hills HILLS --outfile fes.dat

# Plot free energy surface
plumed sum_hills --hills HILLS --outfile fes.dat --kt 2.49 --stride 1000

Advanced Topics

1. Advanced Sampling Methods

PLUMED supports various advanced sampling methods:

  • Metadynamics
  • Temperature Replica Exchange
  • Path Sampling
  • Adaptive Sampling

2. Custom Analysis

Use PLUMED for custom analysis:

  • Free Energy Calculation
  • Reaction Coordinate Analysis
  • Conformation Analysis
  • Dynamics Analysis

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