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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 8
lists performance tuning parameters.
Section 9
explains user defined forces. conformation change calculations.
Section 10
describes collective variable-based calculations.
Section 11
explains alchemical free energy calculations.
Section 12
presents accelerated sampling methods.
Section 13
lists runtime analysis options.
Section 14
provides hints for X-PLOR users.
Section 15
provides sample configuration files.
Section 16
gives details on running NAMD.
Section 17
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
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Next: NAMD and molecular dynamics Up: NAMD 2.8b1 User's Guide Previous: List of Figures   Contents   Index
namd@ks.uiuc.edu