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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
- lists standard minimization
and dynamics parameters.
- Section 7
- 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 12
- lists runtime analysis options.
- Section 13
- provides hints for X-PLOR users.
- Section 14
- provides sample configuration files.
- Section 15
- gives details on running NAMD.
- Section 16
- gives details on installing NAMD.
We have attempted to make this document
complete and easy to understand and to make NAMD itself
easy to install and run.
We welcome your suggestions for improving the documentation or code
at namd@ks.uiuc.edu.
Subsections
Next: NAMD and molecular dynamics
Up: NAMD 2.7b2 User's Guide
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namd@ks.uiuc.edu