http://www.sklogwiki.org/SklogWiki/index.php?title=BRAHMS&feed=atom&action=historyBRAHMS - Revision history2024-03-28T15:54:35ZRevision history for this page on the wikiMediaWiki 1.41.0http://www.sklogwiki.org/SklogWiki/index.php?title=BRAHMS&diff=10468&oldid=prevCarl 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<p>New page: '''BRAHMS''' is a rigid-body <a href="/SklogWiki/index.php/Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a> simulation code. The program is able to efficiently simulate hydrated <a href="/SklogWiki/index.php?title=Lipids&action=edit&redlink=1" class="new" title="Lipids (page does not exist)">lipid</a> bilayers and analyse the trajectories to extract...</p>
<p><b>New page</b></p><div>'''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]]. <br />
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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.<br />
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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.<br />
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==References==<br />
==External links==<br />
*[http://www.personal.soton.ac.uk/orsi/brahms/ BRAHMS Home Page]<br />
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[[Category: Materials modelling and computer simulation codes]]</div>Carl McBride