NAMD-Lite

Overview

NAMD-Lite is a rapid prototyping framework for developing new simulation methods for biomolecules. It is a sequential, C language code base consisting of modular parts that are easy to modify and reuse. The intention is to separate the development of the method from the additional complication due to parallel implementation, providing a simpler way to test and validate new methods before bringing them into NAMD.

The code is a collection of C libraries, the continued development of MDX. The name "MDX" is in the process of being retired in favor of better denoting its relationship as a vehicle for NAMD method development.

Methods

Below is a list of the simulation methods and capabilities available to NAMD-Lite.

  • constant energy - velocity-Verlet, shadow Hamiltonian
  • temperature control - Berendsen temperature bath, Nose-Hoover thermostat
  • energy minimization - conjugate gradient method
  • atom constraints and restraints - harmonic constraints, fixed atoms
  • bond constraints - rigid water using SETTLE
  • force fields - CHARMM (without CMAP), Buckingham potential parameterized for silica (BKS, TTAM, FB)
  • full electrostatics - PME, multilevel summation
  • polarizable force fields - induced point-dipole solved to self-consistency (various parameterizations for water including RPOL, available in dpsim), Drude oscillators using dual-temperature thermostat
  • input file support - coordinate PDB, binary restart, PSF, CHARMM parameter files, X-Plor parameter files, NAMD-style configuration file
  • output file support - coordinate PDB, binary restart, DCD

Source Code and Documentation

This is a source code release only. Building requires GNU Make. There are build files (in the arch/ subdirectory) targeting Linux, Mac OS X, and Solaris (out-of-date). For Mac users, you will need to install the X-Code tools. Building on Windows should also be straightforward using cygwin.

Note that we aren't allowed to distribute FFTW (the fast Fourier transform library that PME depends on) without using a more restrictive license. This means that PME is initially disabled until you follow the instructions to download the library yourself and setup the source packages as expected.

How to Cite

If you use NAMD-Lite for your research, please cite it as follows:

David J. Hardy, NAMD-Lite, http://www.ks.uiuc.edu/Development/MDTools/namdlite/, Universty of Illinois at Urbana-Champaign, 2007.

An example bibtex file is provided that makes uses of the url style package (\usepackage{url}).

Contact

If you have questions please send email to the author David J. Hardy at dhardy@ks.uiuc.edu.

Page created and maintained by David J. Hardy.