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Introduction
NAMD is a parallel molecular dynamics program for UNIX
platforms designed for high-performance
simulations in structural biology. This document describes how to use
NAMD, its features, and the platforms on which it runs.
The document is divided into several sections:
- Section 1
- gives an overview of NAMD.
- Section 2
- lists the basics for getting started.
- Section 3
- describes NAMD file formats.
- Section 4
- explains PSF file generation with psfgen.
- Section 5
- presents the potential functions,
non-bonded interactions, and full electrostatics.
- Section 6
- explains Generalized Born implicit solvent simulations.
- Section 7
- lists standard minimization
and dynamics parameters.
- Section 16
- lists performance tuning parameters.
- Section 8
- explains user defined forces.
conformation change calculations.
- Section 9
- describes collective
variable-based calculations.
- Section 10
- explains alchemical free energy calculations.
- Section 11
- presents accelerated sampling methods.
- Section 15
- lists runtime analysis options.
- Section 17
- provides hints for X-PLOR users.
- Section 18
- provides sample configuration files.
- Section 19
- gives details on running NAMD.
- Section 20
- gives details on installing NAMD.
Subsections
Next: NAMD and molecular dynamics
Up: NAMD 3.0alpha User's Guide
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http://www.ks.uiuc.edu/Research/namd/