Simple Molecular Dynamics Simulation

Constant energy MD simulation of a water molecule (TIP4P water model) between Cl- (yellow) and Na+ (cyan). The ions are tethered to their initial position by a harmonic spring.

The first movie shows every single time step (dt = 1fs) that has been calculated by integrating Newton's equations of motions of the particles. Total simulated time of the movie: 5 ps.

The second movie is more representative of what one normally sees of a MD simulation: Only every 1 ps is saved and visualised. Total time of the simulation is 50 ps (i.e. 50 frames).

(Prepared with VMD and rendered with Tachyon.)

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.html02-Jan-2012 19:52 1.9K 
[TXT]HEADER.html02-Jan-2012 19:52 1.4K 
[VID]water_ions_5ps_dt1fs.mp401-Jun-2011 17:49 5.4MNVE MD simulation: water, Na+, Cl-
[VID]water_ions_50ps_dt1ps.mp401-Jun-2011 17:49 499KNVE MD simulation: water, Na+, Cl-
[VID]water_ions_5ps_dt1fs.avi01-Jun-2011 17:49 12MNVE MD simulation: water, Na+, Cl-
[VID]water_ions_50ps_dt1ps.avi01-Jun-2011 17:48 611KNVE MD simulation: water, Na+, Cl-

Creative Commons License
NVE MD simulation: water, Na+, Cl- by Oliver Beckstein is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

Note for Apple Macintosh users: In order to view the avi movies in QuickTime you might want to install the free open source component bundle from perian.org, which supports many popular video formats, including the mpeg4 format that was used to encode the transitions (using encode_movie.py to drive mencoder).