VMD指导材料---美国伊利诺伊大学

University of Illinois at Urbana-Champaign

Beckman Institute for Advanced Science and Technology

Theoretical and Computational Biophysics Group

Computational Biophysics Workshop

Using VMD

VMD Developer:

John Stone

Tutorial Contributors:

Alek Aksimentiev, Anton Arkhipov, Robert Brunner, Jordi

2

A current version of this tutorial is available at

http://www.ks.uiuc.edu/Training/Tutorials/

Join the tutorial-l@ks.uiuc.edu mailing list for additional help.

CONTENTS 3

Contents

1 Working with a Single Molecule 8

1.1 Loading a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . 8

1.2 Displaying the Molecule . . . . . . . . . . . . . . . . . . . . . . . 9

1.3 Graphical Representations . . . . . . . . . . . . . . . . . . . . . . 10

1.3.1 Exploring different drawing styles . . . . . . . . . . . . . . 10

1.3.2 Exploring different coloring metho ds . . . . . . . . . . . . 12

1.6.2 Increasing resolution . . . . . . . . . . . . . . . . . . . . . 18

1.6.3 Colors and materials . . . . . . . . . . . . . . . . . . . . . 19

1.6.4 Depth perception . . . . . . . . . . . . . . . . . . . . . . . 21

1.6.5 Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

2 Trajectories and Movie Making 25

2.1 Loading Trajectories . . . . . . . . . . . . . . . . . . . . . . . . . 25

2.2 Main Menu Animation Tools . . . . . . . . . . . . . . . . . . . . 26

2.3 Trajectory Visualization . . . . . . . . . . . . . . . . . . . . . . . 27

2.3.1 Smoothing trajectories . . . . . . . . . . . . . . . . . . . . 27

2.3.2 Displaying multiple frames . . . . . . . . . . . . . . . . . 27

3.2 VMD scripting . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

3.2.1 Loading molecules with text commands . . . . . . . . . . 34

3.2.2 The atomselect command . . . . . . . . . . . . . . . . . 35

3.2.3 Obtaining and changing molecule properties with text

3.2.4 Sourcing scripts . . . . . . . . . . . . . . . . . . . . . . . . 39

3.3 Drawing shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

CONTENTS 4

4 Working with Multiple Molecules 42

4.1 Main Menu Molecule List Browser . . . . . . . . . . . . . . . . . 42

4.1.1 Loading multiple molecules . . . . . . . . . . . . . . . . . 42

4.1.2 Changing molecule names . . . . . . . . . . . . . . . . . . 43

4.1.3 Drawing different representations for different molecules . 44

4.1.4 Molecule Status Flags . . . . . . . . . . . . . . . . . . . . 44

5.2.1 Aligning molecules and coloring molecules by degree of

5.2.2 Importing FASTA files for sequence alignment . . . . . . 53

5.3 Phylogenetic Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

6 Data Analysis in VMD 58

6.1 Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

6.2 Example of a built-in analysis tool: the RMSD Trajectory Tool . 60

6.3 Example of an analysis script . . . . . . . . . . . . . . . . . . . . 63

CONTENTS 5

Introduction

on multi-gigabyte molecular dynamics trajectories, its interoperability with a

large number of molecular dynamics simulation packages, and its integration of

structure and sequence information.

Key features of VMD include:

• General 3-D molecular visualization with extensive drawing and coloring

• Extensive atom selec tion syntax for choosing subsets of atoms for display

• Visualization of dynamic molecular data

• Visualization of volumetric data

• Building and preparing systems for molecular dynamics simulations

• Interactive molecular dynamics simulations

• Extensions to the Tcl/Python scripting languages

• Extensible source code written in C and C++