BRAHMS
BRAHMS is a rigid-body molecular dynamics simulation code. The program is able to efficiently simulate hydrated lipid bilayers and analyse the trajectories to extract all major physical parameters characterizing biological membranes. BRAHMS can also be used to simulate pure water via the Soft Sticky Dipole (SSD) potential.
Interactions are computed using a combined cell-subdivision/neighbour-list scheme, which relies on standard periodic-boundary and minimum-image conventions. Dedicated routines have been implemented for the calculation of energies, forces and torques, the integration of rigid-body dynamics, the control of pressure and temperature, as well as for the analysis of the trajectory.
The translational motion of all particles is described by Newton's second law. Lennard-Jones particles (lipid headgroups) are represented as point masses, their position being defined by the coordinates of the mass centres, as is standard practice. Gay-Berne particles (lipid tails) are represented as symmetric rigid bodies, whereas SSD molecules (water) as general, nonsymmetric rigid bodies: the rotational motion is described by Euler's equation, the orientations being represented with rotation matrices. An advanced matrix-based method has been implemented to numerically integrate the equations of motion.