Complete Guide from Installation to Molecular Dynamics Enhanced Sampling
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.
# 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
# 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.
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
# 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
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
PLUMED supports various advanced sampling methods:
Use PLUMED for custom analysis:
Molecular Dynamics
Molecular Dynamics
Molecular Dynamics