PLUMED Tutorial

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

Introduction
Installation Steps
Basic Usage
Advanced Topics