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VMD Tutorial

VMD is a software tool for visualizing molecular dynamics simulations and analyzing molecular trajectories. It allows users to load molecular structure files and trajectory files, manipulate molecular representations, and visualize trajectory animations. Key features include options for various molecular representations, coloring schemes, lighting controls, and playing trajectories at different speeds.

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denny
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372 views22 pages

VMD Tutorial

VMD is a software tool for visualizing molecular dynamics simulations and analyzing molecular trajectories. It allows users to load molecular structure files and trajectory files, manipulate molecular representations, and visualize trajectory animations. Key features include options for various molecular representations, coloring schemes, lighting controls, and playing trajectories at different speeds.

Uploaded by

denny
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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VMD

Visual Molecular Dynamics


SETS Workshop at Syracuse
University July 10, 2012

http://www.rcsb.org/pdb/images/1tnf_bio_r_500.jpg

Installation Instructions
Open your preferred Internet browser, and
navigate to http://www.ks.uiuc.edu/.
From the Software tab, highlight VMD and select
Download.
Select Windows OpenGL, CUDA under the latest
version.

Installation Instructions
Enter the username and password you would
like to create, and click Continue.
A new user registration page will appear. Please
fill this information in, and click Register.
On the next page, agree to the license agreement.

Installation Instructions
Click Save and Run from the dialog box that
appears at the bottom of the next page.

If your computer gives a warning message,


simply click Actions Run Anyway.
On the next page, agree to the license agreement.

Installation Instructions
Click Next when the installation wizard appears.
Choose a preferable location. For most users, the
default location will be acceptable.
On the next screen, click Install, then press
Finish.

What is VMD?
A software tool for visualizing molecular
dynamics.
Free / Open Source
Interactive manipulation of molecules

Why do we use VMD?


Visualize molecular dynamics simulations
Analyze trajectories

Visualize system configurations


Imaging of biological molecules

Features and Options


Load PDB and GRO files
Load XTC and TRR trajectories

Rotate, translate and scale molecular systems


Play trajectories at variable speeds

Features and Options


Create images of molecules and systems
Create movies of trajectories

Change 3D visual representations of molecules


Style: Ribbons, van der Waals, Dynamic Bonds, etc.
Coloring: Residue, Molecule Type, Element, etc.
Lighting: Depth Cueing, Stage Lighting, Shiny, etc.

Using the VMD Interface

Visual Display
Main Controls
Command Prompt

Loading Data into VMD

http://www.rcsb.org/

Molecule 2O61

Loading Data into VMD


Choose a new molecule, or load additional data
into an existing molecule.

Extensive list of file types available

Load multiple molecules at the same time

Visual Representations

http://www.rcsb.org/

Molecule 2O61

Visual Representations
Alter lighting of the display
Different shapes and geometrical
representations
Ribbons, van der Waals, dynamic bonds, etc.

Various coloring schemes


Atom type, residue name, element, etc.

Trajectories and Complex Systems

Trajectories and Complex Systems


Can begin editing display while trajectory is
loading
Rotate, scale or translate the complex system or
molecule while the trajectory is running
Alter speed and steps of the visualization
Show only specific components of a complex
system

Test Your Knowledge


True or False: VMD allows a user to
view their molecular dynamics
simulations and systems.

True

False

Test Your Knowledge


True or False: VMD allows a user to
view their molecular dynamics
simulations and systems.

True

Test Your Knowledge


True or False: A user can only rotate
a molecule or system in VMD.

True

False

Test Your Knowledge


True or False: A user can only rotate
a molecule or system in VMD.

False

Test Your Knowledge


How do you load a trajectory into
VMD for visualization?
File New
Molecule Select
Trajectory File

Molecule Load
Molecule Select
Trajectory File

File New
Molecule Select
Structure Load
Trajectory File

Molecule New
Molecule Select
Structure Load
Trajectory File

Test Your Knowledge


How do you load a trajectory into
VMD for visualization?
File New Molecule
Select Structure
Load Trajectory File

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