Normal modes and MD

[Ivoshiee]

Pande Group has contributed to:
http://www.normalmodes.info/

It may be interesting to observe the MD process, but for at least for me the Java Applet will crash my browsers.

[uncle_fungus]

Yeah, it kills my browser too, which is a shame.

[ChelseaOilman]

Works fine on my Vista machine using IE7.

[Ivoshiee]

Works fine on my Vista machine using IE7.

Report - What do you see?

[Flathead74]

It runs OK on my system.

Windows XP SP2
Firefox 2.0.0.12
Java Version: 1.6.0(build 1.6.0_02-b06)

I see at top of view screen:
Connected to [129.74.155.11:54072]
Mode number: 22

Stick and ball depiction.

[ChelseaOilman]

Report - What do you see?

It's very similar to Jmol

[alancabler]

Works here- XP SP2, java patches current

[uncle_fungus]

Hmm, could be a problem with Linux then

[VijayPande]

We will likely be running this sort of new calculation in FAH with a new core in the short to medium term future.

[7im]

Vista-64, IE7, no java updates = Fails with message: NAME="jmv1"

XP-32sp2, IE6, fully patched java = Popup message to turn off direct draw in java and restart browser. Yes, and restarted, and now it just says Waiting for [129.74.155.11:54533]....]

How long is the typical wait?

[Flathead74]

For me, after clearing Firefox's cache, the load time was less than six seconds.

[bruce]

Report - What do you see?

It's very similar to Jmol

The difference is that this site shows specific atomic motions.

Everybody probably knows that a vibrating object (e.g.-a piano string) vibrates in a way that sounds like a single tone. In fact, it is also vibrating at other frequencies simultaneously, and the mixture of these other frequencies gives it "tone color" which allows you to recognize the difference between a piano and a flute that happen to be playing the same note. When the hammer initially hits the piano string, pretty much every frequency is produced, but they all die out very quickly leaving mostly the fundamental frequency plus a family of weaker pitches often called overtones. This family of frequencies are called the "Normal Modes" of the string.

A piano string is specifically designed to have a relatively simple pattern of Normal Modes that produces vibrations at mostly a single frequency. Proteins (even those with a relatively small number of atoms) have extremely complex patterns of Normal Modes -- most of which defy easy understanding. By displaying the protein vibrating at the frequency of a specific Normal Mode, it's much easier to understand what contributes to that vibration.

In contrast, a protein displayed on the PS3 GUI screen appears to be in random motion and there is no discernible pattern, mostly because all modes are active at the same time and your brain cannot sort them out.