MCPRO

Overview

MCPRO is a specialized Monte Carlo simulation package designed for studying protein systems. It provides efficient algorithms for sampling protein conformations and calculating thermodynamic properties.

Features

Monte Carlo sampling
Protein structure prediction
Free energy calculations
Conformational analysis
Multiple force fields support
Parallel computing capabilities

Installation

Requirements

Fortran compiler (GNU, Intel, or PGI)
MPI library for parallel execution
CMake 3.10+
Optional: Python 3.7+

Installation Steps

Download MCPRO:

git clone https://github.com/MCPRO/mcpro.git
cd mcpro

Configure and build:
```
mkdir build
cd build
cmake ..
make
```

Basic Usage

Example Script

# Load protein structure
load protein.pdb

# Run Monte Carlo simulation
mcrun -n 1000000 -t 300

# Analyze results
analyze -o results.dat

Advanced Topics

Sampling Methods

MCPRO supports various sampling methods:

Metropolis Monte Carlo
Replica Exchange
Umbrella Sampling
Wang-Landau Sampling

Performance Optimization

Parallel computing with MPI
Memory optimization
Load balancing
GPU acceleration

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