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NAMD 2.5b2 User's Guide
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NAMD Molecular Dynamics Software
 
Index
Contents
NAMD Molecular Dynamics Software
Non-Exclusive, Non-Commercial Use License
Contents
List of Figures
Introduction
New features in version 2.5b2
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 paramets
Creating PSF Structure Files
Ordinary Usage
BPTI Example
Building solvent around a protein
List of Commands
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
Alchemical Free Energy Perturbation Calculations
Locally Enhanced Sampling
Pair Interaction Calculations
Pressure Profile Calculations
Translation between NAMD and X-PLOR configuration parameters
Sample configuration files
Running NAMD
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)
Compaq AlphaServer SC
IBM RS/6000 SP
Cray T3E
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