New features in version 1.5

There are two new features in NAMD version 1.5: rigid bonds and moving harmonic restraints.

NAMD allows rigid water, with rigid bond angle and bond lengths, and also rigid bonds between hydrogen and heavy atoms. The SHAKE algorithm is used to correct the position so that the center of mass of the bonded atoms does not move, and the RATTLE algorithm is used to correct the velocity so that the kinetic energy is computed correctly. See section 5.2.5 for more details on the algorithms and page for the controlling parameters.

NAMD provides moving harmonic restraints that allow steered molecular dynamics (SMD) simulations. This feature allows a harmonic restraining force to be applied to a single atom in the simulation and the restraining reference position to be moved. See section 5.1.9 for an explaination of the changes to the force field and page for the controlling parameters.

There have been a number of bug fixes and performance improvements since the previous version. The make file structure has been changed so that NAMD is hopefully easier to build and install. In addition, NAMD now works with DPMTA version 2.7, and the DPMTA source code is distributed with NAMD and built automatically.