Introduction

NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. This document is divided into several sections:

Section 1

gives an overview of NAMD.

Section 2

discusses installing and running NAMD.

Section 3

explains the input and output file formats.

Section 4

describes the NAMD configuration file options.

Section 5

presents the details of what NAMD computes.

For those that wish to modify the NAMD source code, there is a companion document, the NAMD Programming Guide, that explains the design and implementation of NAMD. However, the NAMD User Guide should be sufficient for those that wish to use NAMD without modifying the source.

We have attempted to make both the NAMD User Guide and the NAMD Programming Guide 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 user survey at the end of this section.