We have recently been looking into compression of VRML MD trajectories.
VRML 2.0 offers a mechanism for publishing 3D molecular dynamics (MD) trajectories on the world wide web. Some examples are found below. We will be producing MPEGs of these trajectories as part of a comparison of these two approaches.
The movies here were produced as part of a molecular dynamics study into the effect of increasing aspect ratio on the positional stability of various diamondoid and graphitic structures which could possibly be used as say struts in a nanoscale Stewart platform. We presented the results at the The Fifth Foresight Conference on Molecular Nanotechnology.
We converted molecular dynamics trajectories, saved in our binary format, to VRML 2. The sampling rate used in the conversion is very low: 1 frame/ps. The trajectories were originally saved at 20 frames/ps. This sampling rate is sufficient to capture the low frequency, large amplitude motion of main interest to us. The trajectories are 20 ps long, i.e., 20 frames.
When viewing these movies bear in mind:
These files have only been tested on SGI workstations running IRIX 6.2 using Netscape 4.05 with Cosmoplayer 1.1. They have also been tested on a PC running NT 4.0, Netscape 4.05 and Cosmoplayer 2.1.
Rectangular blocks of three aspect ratios (AR), two cross sections (CS), and two surfaces (S) were used. The possible values for these quantities and some images of the corresponding blocks are given below:
|AR||aspect ratio||1, 10, or 100|
|CS||cross section||uc (unit cell, approx. 0.4nm) or 1nm|
|S||surface termination||C (unterminated) or O,H (Oxygen, Hydrogen)|
|(a) AR=1, CS=uc.||(b) AR=10, CS=uc.|
|(c) AR=100, CS=uc.|
|(d) AR=1, CS=nm.||(e) AR=10, CS=nm.|
The blocks described above were simulated using molecular dynamics at two temperatures (T) and with non-bonded interactions (NB) turned off and on. In some simulations one or two ends of the blocks were constrained (NC) not to move (frozen). The possible values for these parameters are given below:
|T||temperature||150K or 300K|
|NB||non-bondeds||on or off|
|NC||constraints||0, 1, or 2 constrained ends|
Finally, here are the VRML movies. We may add more.
Green button to go, red button to stop ...
The image below shows the results of under-annealing.
The movie below is of the structure above.