Molecular Dynamics
VRML 3D Movies


0 Compression

We have recently been looking into compression of VRML MD trajectories.

1 Introduction

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.

2 Molecular Dynamics Study of Positional Stability

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.

3 Conversion

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.

4 Viewing

When viewing these movies bear in mind:

5 System Requirements

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.

6 Structures

6.1 Blocks

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:

Table 1: Block encoding scheme.
Symbol Quantity Possible Values
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)

Figure1: Unterminated diamondoid blocks (S=C), side view.
uc.unterminated.uc.r45.1.pdb.gif uc.unterminated.uc.r45.10.pdb.gif
(a) AR=1, CS=uc. (b) AR=10, CS=uc.
(c) AR=100, CS=uc.
nm.unterminated.nm.r45.1.pdb.gif nm.unterminated.nm.r45.10.pdb.gif
(d) AR=1, CS=nm. (e) AR=10, CS=nm.

The terminated blocks are the same as above but with Hydrogen added to the 100 surface and Oxygen added to the 110 surface. See the paper for details about why this scheme was chosen. The termination scheme is shown below:

Figure 2: O-bridged, H-terminated diamondoid blocks.
nm.unterminated.nm.r45.1.pdb.end.gif nm.unterminated.nm.r45.1.pdb.end.gif
(a) Side view. (b) End view.

7 Simulations

7.1 Blocks

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:

Table 2: Simulation parameters.
Symbol Quantity Possible Values
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 ...

Table 3: Unterminated blocks (S=C).
No non-bonded interactions (NB=off)
Qty. Value
CS uc nm
AR 1 10 100 1 10 100
T 150K 300K 150K 300K 150K 300K 300K 300K 300K
Sim. X X X X X X X X

Table 4: Terminated blocks.
S=(H, 0).
Qty. Value
AR 1 10 100
Sim. X X X

7.2 Under Annealing

The image below shows the results of under-annealing.

Figure 3: S mode in MD simulation of incompletely annealed diamondoid block.

The movie below is of the structure above.

Table 5: Under annealing.
S=(H, 0).
Qty. Value
AR 1 10 100
Sim. X

The End