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NAMD 2.6 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
New features in version 2.6
NAMD and molecular dynamics simulations
User feedback
Acknowledgments
Getting Started
What is needed
NAMD configuration file
Input and Output Files
File formats
NAMD configuration parameters
AMBER force field parameters
GROMACS force field parameters
Creating PSF Structure Files
Ordinary Usage
BPTI Example
Building solvent around a protein
List of Commands
Example of a Session Log
Basic Simulation Parameters
Non-bonded interaction parameters and computations
Full electrostatic integration
NAMD configuration parameters
Additional Simulation Parameters
Constraints and Restraints
Energy Minimization
Temperature Control and Equilibration
Boundary Conditions
Pressure Control
Applied Forces and Analysis
Free Energy of Conformational Change Calculations
Adaptive Biasing Force Calculations
Alchemical Free Energy Perturbation Calculations
Locally Enhanced Sampling
Pair Interaction Calculations
Pressure Profile Calculations
Replica Exchange Simulations
Translation between NAMD and X-PLOR configuration parameters
Sample configuration files
Running NAMD
Mac OS X Users Must Install the IBM XL C/C++ Run-Time Library
Individual Windows, Linux, Mac OS X, or Other Unix Workstations
Linux, Mac OS X, or Other Unix Workstation Networks
Windows Workstation Networks
BProc-Based Clusters (Scyld and Clustermatic)
SGI Altix
Compaq AlphaServer SC
IBM POWER Clusters
Origin 2000
Memory Usage
Improving Parallel Scaling
NAMD Availability and Installation
How to obtain NAMD
Platforms on which NAMD will currently run
Compiling NAMD
Documentation
Bibliography
Index
About this document ...
namd@ks.uiuc.edu