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

lists basic simulation options.

Section 5

lists additional simulation options.

Section 6

provides hints for X-PLOR users.

Section 7

provides sample configuration files.

Section 8

gives details on running NAMD.

Section 9

gives details on installing NAMD.

We have attempted to make this document and the NAMD Programmer's Guide both complete and easy to understand and to make NAMD itself easy to install and run. Please take a moment to help us improve the documentation and the code by filling out the users' survey at the end of this section.