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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
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Next: NAMD and molecular dynamics Up: NAMD Git-2021-05-06 User's Guide Previous: List of Figures   Contents   Index
http://www.ks.uiuc.edu/Research/namd/