Energy programs.

SANDER

is the basic energy minimizer and molecular dynamics program. This program relaxes the structure by iteratively moving the atoms down the energy gradient until a sufficiently low average gradient is obtained. Structures should usually be minimized before molecular dynamics simulation. The molecular dynamics portion generates configurations of the system by integrating Newtonian equations of motion. MD will sample more configurational space than minimization, and will allow the structure to cross over small potential energy barriers. For complicated systems MD is usually able to locate lower energy conformations than simple energy minimization. Configurations may be saved at regular intervals during the simulation for later analysis.

More elaborate conformational searching and modeling MD studies can also be carried out using the SANDER module. This allows a variety of constraints to be added to the basic force field, and has been designed especially for the types of calculations involved in NMR structure refinement.

SANDER_CLASSIC

is a modified version of sander from Amber5, that is specially optimized for parallel execution on the Cray T3D/T3E, and which contains the "one-window free energy grid" (OWFEG) code for ligand/inhibitor optimization.

GIBBS

is the free energy perturbation program. It is similar to SANDER, but uses the ensemble of generated configurations to calculate the free energy difference between two similar states through either a perturbation or thermodynamic integration approach. The two states are defined by the user in LEaP or PARM.

NMODE

is both a quasi-Newton Raphson second derivative energy minimizer and vibrational analysis program. NMODE can calculate the normal modes of the system as well as numerous thermochemical properties. Other features include the ability to compute "Langevin modes" (normal modes including viscous coupling to a continuum solvent,) techniques to find transitions states as well as minima, and programs to generate "quasiharmonic" modes (sometimes called Principal Component Analysis) from MD trajectories.

ROAR

is a "Penn State" version of sander, that incoporates a variety of features not found in sander itself. The most notable change is the incorporation of the ability to define a part of the system quantum-mechanically, allowing it to interact with other parts of the system that are defined in a molecular mechanics sense. Other features of ROAR include implementation of a Nose-Hoover-chain MD integrator, Ewald summations, and multiple-time-scale integration routines.