CHARMm Principles

Contents

How to Use This Book

Who should use this book

How to find information

Using this book with QUANTA and Insight II books

Typographical conventions

Credits

1. Introduction to CHARMm

Getting started

Understanding CHARMm processes

Commands and command files

Input and output operations

File formats

Converting file formats

Command stream control

CHARMm measurement units

CHARMm array dimensions

2. Preparing Models for Energy Calculations

Constructing and using residue topology files

Using sequence information

Generating and using a protein structure file

Creating a PSF

Modifying a PSF

Modeling hydrogens

Extended-atom model

All-hydrogen model

Generating and using coordinates

CHARMm internal coordinates

Building Cartesian coordinates from internal coordinates

Coordinate arrays

Format of the CHARMm coordinate file

Constructing hydrogen positions

Using parameter files

Ryckaert-Bellemans torsional potential

Example: Parameter file PARM.PRM

Summary examples

Example: Constructing polymer segments joined by a sulfur bridge

Example: Constructing an alpha helix of polyalanine

Example: Generating random conformations of enkephalin

Example: Constructing an N-methylacetamide dimer

Example: Constructing conformations of cyclohexane

References

3. Performing Energy and Force Calculations

Applying the CHARMm energy function

Internal energy terms

External energy terms

Other energy terms

Example: Calculating the initial energies of enkephalin

Minimizing energy

Minimization methods

Convergence criteria

Example: Minimizing enkephalin

Example: Minimizing crambin

References

4. Performing Molecular Dynamics

Understanding molecular dynamics

Temperature

Dynamics time step

Length of trajectory

Running dynamic simulation variants

Langevin dynamics

Stochastic boundary molecular dynamics

Constant pressure and temperature dynamics

Quenched molecular dynamics

Monitoring dynamics simulation output

Coordinate trajectory format

Using time sets and correlation functions

Example: Running enkephalin dynamics

Example: Calculating correlations in enkephalin dynamics

References

5. Setting Constraints and Periodic Boundaries

Setting constraints

Fixed atom constraint

Harmonic atom constraint

Dihedral constraint

Internal coordinate constraint

Distance constraint

SHAKE

Quartic droplet constraint

Example: Creating the alanine dipeptide phi/psi map

Example: Using NOE constraints

Setting periodic boundaries

Using image options in CHARMm

Using crystal options in CHARMm

References

6. Performing Free Energy Simulations

Understanding the relative free energy Hamiltonian

Using free energy calculation methods

Perturbation method

Thermodynamic integration method

Slow-growth method

Running a free energy simulation

Example: Setting up an FES simulation and running dynamics

Applying scaling

Post-processing data

Using umbrella sampling

References

7. Setting Stochastic Boundaries

Basic features

General procedure

Example: Setting up a stochastic boundary