Carl McBride: New page: '''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...

2010-08-04T10:59:49Z

New page: '''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...

New page

'''BRAHMS''' is a rigid-body [[molecular dynamics]] simulation code. The program is able to efficiently simulate hydrated [[Lipids |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 [[SSD model of water |Soft Sticky Dipole (SSD) potential]].

Interactions are computed using a combined cell-subdivision/[[Neighbour lists |neighbour-list scheme]], which relies on standard [[Periodic boundary conditions |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 [[Newtons laws |Newton's second law]]. [[Lennard-Jones model |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 model |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.

==References==
==External links==
*[http://www.personal.soton.ac.uk/orsi/brahms/ BRAHMS Home Page]

[[Category: Materials modelling and computer simulation codes]]

BRAHMS - Revision history

Carl McBride: New page: '''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...