This software is being made available to the molecular modeling community free of charge and includes commented source code and extensive documentation. Added features include rigid bonds and moving harmonic restraints. Updated user guide, also available in HTML form. Modified to work with PVM 3.4 beta. Simplified build process, fewer options to specify, better documentation.
Several bug fixes.
The use of a spatial decomposition scheme combined with message-driven execution achieves load balance and the overlap of communication and computation. To achieve this, NAMD design and implementation is fully documented in the NAMD Programming Guide. We have successfully ported NAMD to all of our UNIX machines, which include HP, SGI, Sun, and Linux, both single processor and shared memory multiprocessor. Thus, simulations can be easily migrated between the two packages, allowing the output of NAMD to be analyzed using X-PLOR or any other tool built for these file formats.