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NAMD 3.0 User's Guide
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NAMD Molecular Dynamics Software
Index
Contents
NAMD Molecular Dynamics Software Non-Exclusive, Non-Commercial Use License
List of Figures
Introduction
NAMD and molecular dynamics simulations
Acknowledgments
Getting Started
What is needed
NAMD configuration file
Input and Output Files
File formats
NAMD configuration parameters
AMBER file and force field support
GROMACS file support
Creating PSF Structure Files
New commands and Functionalities
Ordinary Usage
BPTI Example
Building solvent around a protein
New Commands in the version 2.0
List of Commands
Example of a Session Log
Force Field Parameters
Potential energy functions
Non-bonded interactions
Water Models
Drude polarizable force field
MARTINI Residue-Based Coarse-Grain Forcefield
Constraints and Restraints
Generalized Born Implicit Solvent
Theoretical Background
3-Phase Calculation
Configuration Parameters
Standard Minimization and Dynamics Parameters
Boundary Conditions
Energy Minimization
Dynamics
Temperature Control and Equilibration
Pressure Control
User Defined Forces
Constant Forces
External Electric Field
Grid Forces
Moving Constraints
Rotating Constraints
Symmetry Restraints
Targeted Molecular Dynamics (TMD)
Steered Molecular Dynamics (SMD)
Interactive Molecular Dynamics (IMD)
Tcl Forces and Analysis
Tcl Boundary Forces
External Program Forces
Collective Variable-based Calculations (Colvars)
Overview of Colvars module and links to documentation
Alchemical Free Energy Methods
1
Theoretical Background
Implementation of the free energy methods in NAMD
Examples of input files for running alchemical free energy calculations
Description of a free energy calculation output
Hybrid single-dual topology approach for relative binding free energy calculation of ligand to receptor
Accelerated Sampling Methods
Accelerated Molecular Dynamics
Gaussian Accelerated Molecular Dynamics
Solute Scaling and REST2
Adaptive Tempering
Locally enhanced sampling
Replica exchange simulations
Random acceleration molecular dynamics simulations
Structure based simulations
Hybrid MD-Go Simulation
Running SMOG simulations
Constant-pH Simulations
1
Overview and Theoretical Background
Implementation Details
New Commands and Keywords
Minimal Examples
Hybrid QM/MM Simulations
Division of Labor
Mechanical and Electrostatic Embedding
Covalent Bonds Divided by the QM/MM Barrier
Custom Quantum Chemistry Software
Independent QM Regions
Keywords
Runtime Analysis
Pair interaction calculations
Pressure profile calculations
Performance Tuning
NAMD performance tuning concepts
Non-bonded interaction distance-testing
Translation between NAMD and X-PLOR configuration parameters
Sample configuration files
Running NAMD
Individual Windows, Linux, Mac OS X, or Other Unix Workstations
Linux Clusters with InfiniBand or Other High-Performance Networks
Linux or Other Unix Workstation Networks
Shared-Memory and Network-Based Parallelism (SMP Builds)
Cray XE/XK/XC
Xeon Phi Processors (KNL)
SGI Altix UV
IBM POWER Clusters
CPU Affinity
GPU Acceleration
Xeon and Zen4 Acceleration
Xeon Phi Acceleration
Memory Usage
Improving Parallel Scaling
NAMD Availability and Installation
How to obtain NAMD
Platforms on which NAMD will currently run
Installing NAMD
Compiling NAMD
Documentation
Bibliography
Index
About this document ...
http://www.ks.uiuc.edu/Research/namd/