Supported Applications

Description

a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Usage

Usage Notes

Condensed movie making tips from VMD. The main points:
1. Just load 1 frame for every 1ns of simulation time. A 1 us simulation would only need 1000 frames. The stride feature in the VMD trajectory loader dialog lets you set this (e.g. to 20, if the generated frames are at a rate of 50 ps per frame). Make sure you choose load all frames at once, rather than background. The background option will render frames as they’re loaded.
2. Figure out what region you want to fix in the structure. Get the residue IDs for this. Go to ExtensionsAnalysisRMSD Tool and enter protein and resid START to STOP, then click on Align. This will align the entire structure through all frames and have resids START to STOP as stationary as possible.
3. Use Create Rep to create multiple representations of the structure. The selection box can be used to specify what you want to show. protein and resid START1 to STOP1 START2 to STOP2 ¦ is a common entry. water and within 3 of protein would show all water molecules within 3A of an atom associated with a protein. You can then play with the different kinds of views (coloring, style, transparency) for each representation individually.
4. Clicking on a representation will show or hide it.
5. For each representation, set the Trajectory to smooth over several frames. I have found that a 4ns smoothing window reduces the jitter without eliminating interesting side chain motion. YMMV.
6. Set DisplayRendermodeGLSL to do OpenGL/CUDA rendering. This should make a big difference. I haven't done a formal test of this, but my laptop, with 48 CUDA 3 processing cores, seems to do much better, smoother, and faster rendering than my Mac Pro (which does not have a compatible CUDA card).

Movie Making:
* loaded every 20th frame (about 1000 from 20k) * smoothing window of 4 * internal Tachyon ray tracer * image smoothing on * half size reduction * 30 FPS (NTSC) * MPEG output
Apparently a good trick to get nice looking animations is to double therendering window; then set the movie generator to half-size the result. I guess this gives a per-frame image smoothing effect as thepotentially hard edged rendered image is reduced to an anti-aliased frame.

Installation

Primary Citation*

W. Humphrey, A. Dalke, and K. Schulten. 1996. VMD - Visual Molecular Dynamics. Journal of Molecular Graphics. 14: 33-38.

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  *Full citation information available through

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Citation Note

Tales

Computing Cellular Clockworks

Physicist Klaus Schulten once imagined becoming a dancer, relying on nothing but his own mind and body to perform. “But I was not a good dancer,” he says. “So my next thing was theoretical physicist. Just myself, pencil and paper — and in my case, also an eraser.”

That dream was also thwarted. Today, Schulten relies on some of the most powerful and expensive computing equipment on earth to carry out his work, which applies theoretical physics to the understanding of biological systems. His most recent work involved the molecular simulation of an organelle that converts light energy to chemical energy inside a photosynthetic bacterium using the molecular dynamics tools NAMD and VMD, which his lab develops. Looking forward, he wants to simulate an entire living cell, right …

Read the full story here.

Webinars

Topic: VMD: Preparing, Analyzing, and Visualizing Molecular Dynamics Simulations

Presenters: John Stone, University of Illinois Urbana-Champaign and Abhishek Singharoy, Arizona State University


Host: Jason Key
Date Recorded: January 28, 2020

Topic: xMDFF, a new molecular dynamics flexible fitting-based approach.
Presenter: Abhishek Singharoy, Postdoctoral Fellow, Beckman Institute and University of Illinois at Urbana Champaign.

Host: Jason Key
Recorded on December 6, 2016