NAMD: Molecular Dynamics
From Debian Clusters
Contents |
About NAMD
NAMD molecular dynamics project out of the Theoretical and Computational Biophysics Group at University of Illinois at Urbana-Champaign. The project is based on Charm++ and uses VMD for molecular graphics. At the time of this writing, the most current version is 2.6.
This tutorial will cover building NAMD and charm++ for MPI rather than "net-linux".
Building the whole project requires multiple steps:
- Installing the support packages (shown below)
- Building and testing charm++
- Building namd
- Building vmd
Also, I have a page with all of the errors I encountered while figuring out this process. If you follow the tutorials, hopefully you shouldn't see them, but sometimes it's easy to miss a step.
Support Packages
Most of NAMD will need to be installed from source, but two supporting packages can be installed with apt: fftw and tcl.
FFTW is responsible for doing optimized Fourier transforms. To get it, run
apt-get install fftw3 fftw3-dev sfftw-dev sfftw2
Note that fftw3 is a virtual package. When you try to apt-get it, Debian installs libfftw3-3 for you instead. This is fine.
Next, we need Tcl, the "Tool Command Language," which will give additional functionality to NAMD. Install it with
apt-get install tcl8.4 tcl8.4-dev
This will need to be done on each of the worker nodes. You can do it by hand or visit the Cluster Time-saving Tricks page to learn how to write a script to automate it.
Next...
Next, continue on to building and testing charm++.
