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Introduction
VMD is a molecular graphics and visualization program designed to
be used for interactive display of molecular systems, particularly
biopolymers such as proteins, nucleic acids, and biological
assemblies such as membrane lipid bilayers. VMD has several goals:
- General molecular visualization
This program is at heart a general application for graphical display
of molecules, similar in basic capabilities to commercial program
such as Quanta and non-commercial programs such as
XMol, Ribbons, and others. The goal of VMD is not to become a complete replacement for these programs; instead,
VMD focuses on accomplishing the specific goals outlined here.
- Visualization of dynamic molecular data
VMD can display
in a variety of ways dynamically varying quantities for a molecule,
such as position, velocity, and energy. Each molecule
displayed by VMD consists of an animation list, which is
comprised of individual frames of the molecule's trajectory as
computed by some means (molecular dynamics, energy minimization,
etc.). This animation list can be edited, played back, or saved to a
file in a variety of formats. This dynamical data may be obtained
from previous computation, or may be obtained directly from a
concurrently running simulation.
- Display and control of molecular dynamics simulations
VMD contains the ability
to act as a graphical front end for a molecular dynamics (MD) program
running on a remote supercomputer or high-performance workstation.
This allows the user of VMD to set up, initiate, and interactively
display and control the MD simulation as it is running. The user can
disconnect from the simulation and let it continue, or
interactively kill the simulation program and start another. Any
number of simulations may be simultaneously displayed and controlled
by a single VMD session.
- Support for several input and display (output) devices
Beyond the standard workstation monitor and keyboard +
mouse display and input devices available for graphical workstation
users, a number of different visual display and control systems are
available. For example, spatial tracking devices are available which
may be used as a three-dimensional pointer, and stereo image
projection devices are possible which may be used to display a
three-dimensional image of a molecular system to a
number of viewers. VMD supports the use of the two example devices
described here, and aims to make support for other such devices
relatively simple.
- Provide an easily modifiable and extendible program
VMD is written in C++ and employs an object-oriented design to make
the program easy to modify and extend. This Programmer's Guide is
specifically designed to aid those people who are interested in
changing the current implementation of VMD, or who are interested in
adding new features to the program.
This manual, along with
the Users Guide and Installation Guide, document the use of VMD.
A major intention of this manual is that it be kept up-to-date with
all changes to VMD. As features are changed, these changes
should be reflected in the description here, and as new capabilities
are added these new features should be added to the relevant section
in this document. In particular, when new object classes are added
or when existing ones are changed or augmented, the description of
the relevant class should be updated in the `Program Structure' and
`Class Descriptions' chapters. In this way, other uses can also
benefit from new additions. This is a major goal for VMD, to become a
useful, common resource for all users in the field of computational
structural biology.
Subsections
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