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VMD: Visual Molecular Dynamics


William Humphrey, Andrew Dalke, and Klaus Schulten
Theoretical Biophysics Group, University of Illinois and Beckman Institute, Urbana, Illinois 61801

computational tools for molecular visualization and analy-


VMD is a molecular graphics program designed for the sis. Several excellent packages exist for the graphical dis-
display and analysis of molecular assemblies, in particular play of static molecular structures, such as RIBBONS, ~
biopolymers such as proteins and nucleic acids. VMD can XMol, 2 MIDAS, 3'4 SETOR, 5 GRASP, 6 and others. Molecu-
simultaneously display any number of structures using a lar dynamics (MD) studies of the function of the structurally
wide variety of rendering styles and coloring methods. Mol- known biopolymers are being widely applied. The results of
ecules are displayed as one or more "representations," in such studies, however, are typically large molecular trajec-
which each representation embodies a particular rendering tory files, which represent substantial amounts of dynamical
method and coloring scheme Jor a selected subset of atoms. data that require suitable visualization tools, e.g., to initiate
The atoms displayed in each representation are chosen us- molecular dynamics simulations and to display sequences of
ing an extensive atom selection syntax, which includes structures. The increased speed and parallelization of com-
Boolean operators and regular expressions. VMD provides puters make it possible today to carry out molecular dynam-
a complete graphical user interface for program control, as ics studies interactively, in order to probe key properties of
well as a text interface using the Tcl embeddable parser to biopolymers such as potential energy barriers along chosen
allow for complex scripts with variable substitution, control reaction pathways. This approach requires a new molecular
loops, and function calls. Full session logging is supported, graphics user interface.
which produces a VMD command script for later playback. The program VMD has been developed for interactive
High-resolution raster images of displayed molecules may graphical display of molecular systems, in particular bio-
be produced by generating input scripts for use by a number polymers such as proteins or nucleic acids. The motivation
of photorealistic image-rendering applications. VMD has for the development of VMD has been to provide a well-
also been expressly designed with the ability to animate documented and freely available program that is easy to use
molecular dynamics (MD) simulation trajectories, imported and modify, and which addresses several challenges in mo-
either from ,files or from a direct connection to a running lecular graphics, including the following:
MD simulation. VMD is the visualization component of Support for the display of dynamic data such as molecu-
MDScope, a set of tools .for interactive problem solving in lar trajectories generated by molecular dynamics calcu-
structural biology, which also includes the parallel MD lations
program NAMD, and the MDCOMM software used to con- Direct interaction with a separate molecular dynamics
nect the visualization and simulation programs. VMD is application, in order to provide a graphical user interface
written in C++, using an object-oriented design; the pro- and visualization console for the simulation program
gram, including source code and extensive documentation, The capability to work with three-dimensional, immer-
is freely available via anonymous ftp and through the World sive display devices such as a large-screen stereo projec-
Wide Web. tion facility
Text-based as well as mouse-based user interface con-
Keywords: molecular modeling, molecular dynamics visu- trols, including user-customizable menus and program
alization, interactive visualization extensions using an interpreted scripting language
Display of molecules in a wide range of rendering styles
INTRODUCTION easily selected by the user
Production of high-quality hardcopy images of currently
The burgeoning number of experimentally resolved biomo- displayed molecular systems
lecular structures has resulted in an increasing need for We describe in this article the features and structure of
Color Plates for this article are on page 27 and 28.
the program VMD, first mentioning the current implemen-
tation of the program, and then discussing the major pro-
Address reprint requests to Dr. Schulten at the Theoretical Biophysics
gram capabilities and functionality. We also describe the
Group, University of Illinois and Beckman Institute, 405 North Matthews,
Urbana, Illinois 61801. E-mail: kschulte@ks.uiuc.edu use of VMD, coupled with a large-screen stereo projection
Received 17 October 1995; revised 21 December 1995; accepted 11 Janu- system, as a collaborative tool for several researchers to
ary 1996. employ for analysis and discussion of molecular assemblies.

Journal of Molecular Graphics 14:33-38, 1996


1996 by Elsevier Science Inc. 0263-7855/96/$ 15.00
655 Avenue of the Americas, New York~ NY 10010 PII S0263-7855(96)00018-5
Finally, we discuss the use of VMD for interactive molecu- connectivity for each atom is determined by VMD through
lar dynamics modeling, and list the current availability of a nearest-neighbor distance search. VMD understands the
documentation and source code. CHARMm,~/X_PLORm compatible PSF protein struclnre
file fl)rmat, and the Brookhaven PDB t~ coordinate file for-
mat. In addition to molecular file lkwmats, VMD can read
IMPLEMENTATION and display images in Raster 3D ~-~ input file format.
Owing to the large number of molecular data file formats
VMD is written in C++ using an object-oriented design that
currently in use, VMD implements an imerface to the pro-
assists maintenance of the program and the addition of new
gram Babel ~ to read data from formats other than PDB or
features. The distribution of VMD includes documentation
PSF. If Babel is installed, it is used to convert files from
describing how to compile, install, use, and modify the pro-
alternate lormats into PDB format before being read by
gram for different hardware and software configurations.
VMD. This also includes multiple-coordinate-set data files,
VMD requires either the Silicon Graphics GL library or the
such as those in XYZ fornml.
OpenGL library for three-dimensional graphics rendering.
A key feature in VMD is the abilil~ to work with mo-
A sample VMD session is shown in Color Plate 1, which
lecular dynamics simulation programs, and to display the
illustrates the three components of the user interface: the
simulated molecule am its motion is computed (as discussed
graphics display window, the graphical user interface win-
below). Thus, new structures may be loaded into VMD
dows, and the VMD console. On the right in Color Plate I
through connection to a running simulation, instead of being
is the graphics display window, in which molecules are
read from a file. Once loaded, however, a structure obtained
rendered and interactively rotated, translated, and scaled via
from a network connection is treated in the same manner as
mouse controls, A user-customizable pop-up menu is avail-
if read from disk.
able in this window. The image shown in the graphics dis-
play window is referred to am the current scene. VMD con-
tains options for rendering the scene to a high-quality raster Animating molecular structures
image file am described below,
VMD uses XForms v for the graphical user interface, For each molecule displayed by VMD there is an associated
which uses a collection of.fiwms to represent the graphical animation li.~t, which is a collection of atomic coordinate
controls available to the user. Examples of some of the sets for the molecule. Controls are awfilable to play back the
forms available in VMD are shown on the left in Color Plate trajectory, with options to control the animation speed,
I. The graphical user interface (GUI) in VMD includes a fl'ame increment, and animation direction. New trajectory
toolbar that provides access to the specific torms for tasks coordinate sets may be read fl'om PDB files, or from DCD
such am changing the current molecular display characteris- files binary c o m p a t i b l e with the m o l e c u l a r d y n a m i c s /
tics or animating selected molecules using molecular dy- refinement programs C H A R M m '~ and X-PLOR. io These co-
namics trajectories. ordinate sets may be loaded when the rnolecule is initially
Below the graphics display window in Color Plate I is the read into VMD, or may be loaded later. A molecuh.~r tra-
VMD text console, which displays informative messages jectoqr editor is also available, with options to delete spe-
and provides a command prompt fbr keyboard control of the cific fl'ames or met of frames from lhe animation list, and to
program. All actions in VMD are available via text com- write coordinate sets to files.
mands: full session logging and playback are possible. Us-
ers can wrile scripts that may be run at any time, and that
can be executed, for example, by entering a short text com- Displaying molecular structures
mand or through a user-customized pop-up menu selection. Any number of molecules may be displayed and manipu-
VMD employs Tel, s an embeddable interpreted script lan- lated in the graphics display window, as shown in Color
ouage parser, to process text commands. Tcl provides a full Plate I. Each structure is drawn as several relnwSenlations.
met of scripting capabilities for the program, and makes or views, of the molecule. Multiple views of a molecule may
possible complex features such as variable substitution, be shown simultaneously to create a complex image of the
conditional expressions, control loops, and subroutines. A system. A view is just one particular method of drawing the
user-customizable configuration file is read when V M D molecule, and consists of three characteristics:
starts up, which may be used to define a personalized V M D
working environment and to define new commands and 1. An atom subset selection, which determines which atoms
program extensions, as well as to create customized pop-up are to be included in the view
m e n t l controls. 2. A remlering, style, which determines the primitives used
to draw the atoms, bonds, and other molecule compo-
nents. Table I I <' lists many of the rendering styles avail-
CAPABILITIES able in VMD
3. A colorinv lnethod, which determines what color to use
New molecules are read into V M D from a set of molecular for the components of the view. Numerous coloring
structure/coordinate files, or may be read from a mingle co- methods are available, some of which are listed in Ta-
ordinate file. The molecular structure file contains static ble 2
information about the system, such as bond connectivity
and atomic mass and charge values. The molecular coordi- Views are created or modified xia text commands or,
nate file contains the positions of all the atoms that make up more easily, by using the graphical interface controls. Color
the molecule. When a structure file is not provided, the bond Plate 2 shows a detailed representation of a protein dimer

34 J. Mol. Graphics, 1996, Vol. 14, February


Table 1. Selected molecule-rendering styles available in or off, and may be interactively moved to new positions
VMD with the mouse.

Style Description
Raster image generation
Lines Simple lines for bonds; points for atoms An interface to a number of image-rendering packages is
Bonds Lighted cylinders for bonds; no atoms provided in VMD and can be used to create input scripts for
VDW Solid, lighted van der Waals spheres for use by these programs. The generated input scripts may then
atoms; no bonds be read by the selected package, to create a raster output
CPK Scaled van der Waals spheres for atoms; image of the graphics scene displayed by VMD suitable for
cylinders for bonds publication or slides. Table 3 lists the currently supported
Dotted Dotted van der Waals spheres for atoms; no image-rendering packages.
bonds The capability to create input scripts for image-rendering
Licorice Solid spheres and cylinders with equal radii programs may be combined with the Tcl scripting language
Tube Cylindrical tube through C,~ atoms ~ available in VMD to easily create high-quality movies of a
Ribbon Flat ribbon through C,~ atoms" molecule. As an example, the following script may be used
Surf Solvent-accessible surface of selected atoms b to create a series of images showing a previously loaded
Caaoon Simplified secondary structure molecule rotating about the Y axis, by creating input scripts
representations for the Raster3D ~2 program that are processed immediately
after they are created:
For nucleic acids, the P atoms are used.
bUsing the SURF algorithm t3a developedat the Universityof North Caro-
lina. ### Tcl script to create a R a s t e r 3 D m o v i e
### of a rotating m o l e c u l e
complexed with a segment of DNA. Molecules may be for [ set i 0 ] [ $i < 360 }
displayed using either an orthographic or a perspective pro- [ set i [ expr $i + i0 ] l [
jection. ### create and process a R a s t e r 3 D s c r i p t
set scriptfile "rotate.$i.r3d"
The atom selection capabilities of VMD are quite exten-
set imagefile " r o t a t e . $ i . r g b ~
sive, and include a flexible syntax for complex selection render R a s t e r 3 D S s c r i p t f i l e
expressions. Each atom in a molecule has several charac- catch [ exec render < S s c r i p t f i l e -sgi
teristics; keywords are used to select the atoms that have $imagefile ]
values matching a specified criterion. For example, each ### rotate the current image by i0 degrees
atom has a set of character string names, an (x, y, z) position, ### about the Y axis
and other numeric values such as charge and mass. Each rot y by i0
atom also has Boolean characteristics identifying it, for ex- ]
ample, as a member of an amino acid or nucleic acid or as
part of the protein backbone. Boolean operations may be After loading a molecule, this script would be invoked sim-
used to select atoms based on multiple characteristics, and ply by typing (assuming it was in a file called movie.tcl)
parentheses may be used to select the order of evaluation.
For example, the selection
Table 2. Selected molecule-coloring styles available in
(resname ASP or resname GLY) and mass > ii
VMD

selects all atoms that are in aspartic acid or glycine residues, Style Description
and that have a mass greater than 11. Similarly, the selection
Name Color determined by atom name
Resname Color determined by residue name
backbone and within 8 of resid i00
Segname Each segment shown in a different color
Molecule Each molecule shown in a different color
selects all backbone atoms that are within 8 units (e.g., Chain Color determined by one-character chain
within 8 ,~) of residue 100. Regular expressions may be identifier
used in strings to specify quickly many different names in a Beta Color scale based on the beta values of
selection. When a selection changes during a trajectory the PDB file
(such as the atoms within some radius of another set of Occupancy Color scale based on the occupancy val-
atoms), the user can request an update of the selection each ues of the PDB file
time a new animation time step is displayed. Mass Color scale based on the atomic mass of
When displaying solid objects, VMD can make use of each atom
available hardware-accelerated lighting capabilities, a capa- Charge Color scale based on the atomic charge of
bility exploited in other molecular visualization packages each atom
such as SETOR. 5 Up to four independent, infinitely distant Pos Color scale based on the distance of each
light sources may be positioned in the scene and used to atom from the center
illuminate the displayed objects. Each light can be turned on

J. Mol. Graphics, 1996, Vol. 14, February 35


Table 3. Available rendering program output formats environment to provide a natural problem-solving environ-
ment for structural biology. The goal of these enhancements
Name Description is to help "untie" the users from the keyboard, to make
possible manipulation and analysis of molecular structures
Raster3D Fast raster file generator by several collaborators at the same time in a natural work-
POV Persistence of Vision ray tracing package ing environment. The user interface controls of VMD are
Rayshade Rayshade ray tracing package being updated to make use of each available 3D pointer as
Radiance RADIANCE lighting simulation and ren- a 3D mouse, that would be used for rotation and control of
dering system the molecules just as the normal, 2D mouse is used. Also
ART VORT ray tracer being explored are an audio user interface to allow users to
issue spoken commands. User interface controls such as
these may eventually replace or augment keyboard and
menu controls.
play movie.tcl. More complex transformations are per-
formed in a similar manner.
Trajectory analysis tools
VMD includes functions for analyzing molecular structures
Stereo display
and trajectories. These functions access the internal VMD
The scene displayed in the graphics window may be ren- data structures to return or modify characteristics such as
dered in stereo, to enhance the appearance and information charge, mass, and position for individual atoms, residues,
content of the displayed systems. The stereo viewing pa- and molecules. More complex analysis capabilities, such as
rameters, which include the eye separation distance and the computing the RMS deviation or correlation functions of a
focal length, can be interactively controlled by the user. dynamics trajectory, can then be implemented as Tcl scripts
Two stereo display formats are available in VMD: without the need to modify the VMD source code.
As an example, the following commands illustrate the use
1. A side-by-side stereo display, which splits the display of the VMD analysis language to query and change the
window into two halves, a left-eye view and a right-eye center of mass of a specific residue. The first step is to
view. This format may be used with all graphics display create an atom selection and bind it to an identifier:
hardware, and is suitable for preparing images for pub-
lication.
2. A crystal-eyes stereo display, which utilizes special vmd > set my_sel [atomselect top ~resid 3"]
hardware available on many graphics workstations to
display stereo images to be viewed with liquid crystal- Information about the atoms in this selection may then be
shuttered glasses. retrieved using the " g e t " option:

The stereo viewing modes may be used with standard vmd > Smy sel get [name mass x y z}
display monitors, or with external stereo display equipment. Info) [N 14.007 1.488 2.280 -0,863]
As an example, VMD is currently being used with a three- [H 1.008 0.770 1.998 -1.467]
dimensional projection system for the display and analysis [CA 12.011 1.981 3.643 --0.909}
of molecules viewed simultaneously by several users. This {CB 12.011 1.147 4.464 --1.880}
system consists of a ceiling-mounted projector, echoing [C 12.011 1.865 4.326 0.444]
onto a large (6 by 8 foot) screen the stereo images displayed {O !5.999 2.801 4.963 0.924}
on a graphics workstation monitor. The large-screen display
makes it possible for many viewers to study collaboratively Using these atom selection commands, and a set of vector
at a large magnification a biopolymer system; the stereo manipulation procedures implemented in Tcl, the function
display environment enhances the information content of to compute the center of mass of a selected set of atoms is
the scene through the addition of visual depth cues. VMD then realized as follows:
contains several options to configure the graphics display
for use with large-screen projection systems, e.g., to set the ### Tcl p r o c e d u r e to compute the center of
projection screen vertical and horizontal dimensions. ### mass of a set of a t o m s
One problem encountered when several people view the proc com {sel] [
same computer-generated stereo image is that each person set a t o m s [$sel get [mass x y z]]
sees the scene from a different perspective. To help alleviate s e t totalMass 0.0
this problem, VMD supports the use of spatial tracking s e t com [veczero]
foreach atom Satoms [
devices (such as the Polhemus Fastrak [Polhemus Inc., Col-
s e t m a s s [lindex Satom 0]
chester, VT]) that measure the 3D position and orientation
s e t pos [irange Satom 1 3]
of sensors relative to a fixed position, in order to provide a s e t totalMass [expr S t o t a l M a s s + Smass]
set of 3D pointers, VMD displays visual representations of set com [vecadd $com [vecscale Smass $pos]]
the pointers on the screen, such that all viewers perceive the ]
pointers at the same positions relative to the molecules. return [vecscale $com [expr 1.0 /
New features and user interface methods are currently StotalMass]l
being added to VMD for use with this stereo projection l

36 J. Mol. Graphics, 1996, Vol. 14, February


The application of this procedure is straightforward; execut- connection between VMD and a running simulation may be
ing the new command " c o r n " with a previously defined dropped and later reestablished, e.g., to allow a user to
atom selection identifier as an argument returns the center check on the progress of a running simulation without hav-
of mass of the atoms in that selection: ing to stop and restart the calculation. Molecules displayed
in this manner may also be manipulated and rendered in the
vmd > com $my sel same fashion as molecules loaded from data files, and trans-
Info) 4.59783 5.14667 4.275 ferred molecular structures may be saved in an animation
list for storage and playback.
This information could then be used, for example, to move
the center of mass of the atoms to some other position, for
example to the origin:
Example of use

Color Plate 3 illustrates an example of the use of VMD for


vmd > Smy_sel moveby [vecinvert [corn $sel] ] interactive molecular dynamics. The first step in establish-
ing a connection to a running simulation is to select a host
computer, and to choose between starting a new simulation
In addition to the calculation of center of mass motion,
or reconnecting to a running job (Color Plate 3a). The initial
several other Tcl procedures are available in VMD for dy-
connection to the host computer returns the lists of available
namic trajectory analysis including computation of RMSD
applications and running simulations from a daemon run-
values, autocorrelation functions, and Ramachandran plot ning on the host computer. Selecting an available applica-
(qb-qJ angle) data. New analysis functions can be easily
tion in order to start a new simulation (in this case a simu-
developed and added to VMD by the user.
lation using NAMD) results in VMD requesting from the
host computer the list of parameters necessary to start the
job (Color Plate 3b). Once all the parameters are entered,
INTERACTIVE MOLECULAR DYNAMICS the simulation program is launched, and the static molecular
structure data are returned to VMD. As the molecular tra-
VMD is designed to act as a visualization console and jectory is computed, the coordinate sets are sent to VMD for
graphical front end for a molecular dynamics application display (Color Plate 3c). The available graphical user inter-
running on a remote supercomputer or high-performance face controls may be used to view or modify simulation
workstation. VMD uses a set of daemons and library rou- parameters or display characteristics, or to terminate the
tines, known as the M D C O M M software, to broker the simulation. Color Plate 3c also shows several atoms to-
communication of data and commands between VMD and a gether with the applied forces, the latter specified by the
remote simulation program. The M D C O M M software in- user with the mouse (the horizontal and vertical arrows).
terface is independent of the particular remote application; These forces have transformed the small polypeptide from
the daemons buffer data transfer between the application an alpha helix conformation to the form shown in Color
and VMD, and act as managers for the running jobs and Plate 3c.
interprocess communication. Once a particular simulation Once a connection to a running simulation has been es-
p r o g r a m has been suitably modified to work as an tablished, VMD provides options to modify simulation pa-
M D C O M M client, VMD can be used with that program rameters, such as the temperature, and remote connection
without change. parameters, such as the frequency with which coordinate
VMD is the visualization component of a larger set of sets are communicated from the simulation program to
computational tools for structural biology known as VMD. The user can also directly participate in the simula-
M D S c o p e . ra M D S c o p e includes not only V M D and tion through the addition of perturbative or guiding forces to
MDCOMM, but also the parallel molecular dynamics pro- selected atoms or residues, a feature developed and studied
gram NAMD. ~5 N A M D is a parallel, portable molecular earlier in the program SCULPT.~6 Forces are added using
dynamics program written in C++, which implements the the mouse to indicate the magnitude and direction of the
C H A R M m force field 9 and contains numerous simulation additional interaction on selected atoms; these forces are
options. NAMD uses a spatial decomposition algorithm to communicated to the simulation program and incorporated
distribute the computation tasks among parallel processors, into the dynamics.
which partitions the volume of space occupied by the simu- The use of interactive guiding forces in simulations of
lated molecule into uniform cubes, known as patches, as- biomolecular systems is currently being applied or consid-
signed to different processing nodes. While NAMD and ered tbr a number of projects. Two systems being examined
VMD may be used independently of each other, taken to- with these interactive tools are the protein bacterio-
g e t h e r , V M D , N A M D , and M D C O M M c o n s t i t u t e rhodopsin, and the binding of biotin to the protein avidin.
MDScope. Information on MDScope may be obtained from For bacteriorhodopsin (bR), a 26-kDa membrane protein
the MDScope W W W home page, http://www.ks.uiuc.edu/ used to convert light energy into a proton gradient for ATP
Research/mdscope. synthesis in Halobacterium halobium, 17 molecular dynam-
VMD provides an interface to initialize a new simulation, ics simulations are being performed using interactive forces
and can serve also to monitor and control certain simulation to guide the positioning of water molecules near key resi-
parameters. After a simulation is started and a connection dues. Such water molecules could not be resolved in the
between VMD and the application is made, molecular struc- experimentally determined bR structure, but are considered
tures are communicated to VMD as they are calculated. The to play key roles in the proton transfer mechanism of bR.

J. Mol. Graphics, 1996, Vol. 14, February 37


Interactive forces are also being considered for the study of Minnesota Supercomputer Cenier, Inc., Minneapolis,
the interaction of the 32-atom biotin vitamin with the pro- Minnesota, 1993
tein avidin. Avidin is a 15.6-kDa protein found in tetrameric 3 Ferrin, T.E., Huang, C.C., Jarvis, L.E., and Langridge,
form in animal and reptile egg white, which has a strong R. The MIDAS database system..I. Mol. Graphics 1988,
binding affinity for biotin. TM lnteractively applied forces 6, 2-12
could be used to pull biotin from the binding site in avidin, 4 Ferrin, T.E., Couch, G.S., Huang, C,C., Pettersen, E.F..
in order to shed light on the molecular mechanism of how and Langridge, R. An affordable approach to interactive
avidin accommodates the biotin structure. desklop molecular modeling../. Mol. Graphics 1991, 9,
27-32
5 Evans, S.V. SETOR: Hardware lighled three-dimen-
DOCUMENTATION
sional solid model representations of macromolecules.
Extensive documentation on how to use the visualization ,I, Mol. Graphics 1993, I1, 134 138
features of VMD and how to modify and extend the pro- 6 Nicholls, A., Sharp, K., and Honig, B. Protein folding
gram is available. The following documents, in PostScript and association: Insights from the interfacial and ther-
format, are provided via anonymous tip: modynamic properties of hydrocarbons. Proteins.
t an installation guide, describing how to compile and in- Strm't. f'tmction Genet. 199 I, 11, 282-290
stall VMD 7 Zhao, T.C. and Overmars, M. Forms Library .fi)r X.
a user's guide, explaining the capabilities and features of http://bragg.phys.uwnl.edu/xforms. 1995
VMD 80usterhout, J. 77'l and the Tk Toolkit. Addison-Wesley,
a programmer's guide, listing the structure and layout of Reading, Massachusells. 1994
VMD and indicating how to add new capabilities 9 Brooks, B.R., Bruccoleri, R.E., (-)lafson, B.D., Stales,
D.J., Swaminathan, S., and Karplus, M. CHARMm: A
An on-line feature is also available. program for macromolecular energy, nfinimization, and
dynanfics calculations. ,/. Compul. Chem.. 1983, 4, 187-
AVAILABILITY 217
1() Brtinger, A.T., X-PLOR. The Howard Hughes Medical
The complete set of source code and documentation files for Institute and Department of Molecular Biophysics and
VMD, as well as a precompiled binary for Silicon Graphics Biochemistry, Yale University, New Haven. Connecti-
workstations, is available free of charge for noncommercial cut, May 1988
use via anonymous ftp from the ftp server ftp.ks.uiuc.edu, in
11 Bernstein, F,C. The protein data bank: A computer ar-
the directory/pub/mdscope/vmd. Up-to-date information on
chive. ,I. Mol. Biol. 1977, 112, 535 542
VMD may be obtained by accessing the VMD WWW home
12 Merritt, E.A. and Murphy,, M.E,P. Raster3D version
page, http:llwww.ks.uiuc.edu/Researchlvmd. VMD is avail-
2.0--a program for photorealistic nlolecuhir graphics.
able primarily for Silicon Graphics workstations, running
Acta Crv~'tallogr. D 1994, 5II, 869-873
version 5 or later of the IRIX operating system. The pro_
gram has also been compiled and run on Hewlett-Packard 13 Waiters, P. and Stahl, M. Babel. version 1. I. University
PA-R1SC workstations running version 9 of the HP-UX of Arizona, Tucson, Arizona, 1992
operating system, and on IBM RS-6000 workstations run- 13a Varshney, A., Brooks, F.P., and Wright, W.V. Linearly
ning AIX. scalable computation of smooth molecular surfaces.
IEEE Cosnp. Graphics Appl. 1994. 14, 19-25
14 Nelson, M., Humphrey, W., Gursoy, A., Dalke, A.,
ACKNOWLEDGMENTS KahS, L., Skeel, R., Schultcn, K., and Kufrin, R.
We thank all contributors to VMD, including Ken Hamner MDScopc--a visual computing environment for struc-
and Jim Phillips at the University of Illinois, and Jon Leech tural bioh)gv. Comlmt. Phv,v. Commim. 1995, 91, I I 1
at the University of North Carolina, as well as the main 134
authors of NAMD, Mark Nelson, Attila Gursoy, and Robert 15 Nelson, M., Humphrey, W., Gursoy, A., Dalke, A.,
Brunner. Special thanks go to Rick Kufrin of the National Kale, L., Skeel, R.D., and Schulten, K. N A M D - - a par-
Center for Supercomputing Applications, the author of the allel, object-oriented molecular dynamics programn. J.
MDCOMM software. We also thank the members of the Stq~ercomput. AI)pI. 1996 (in press)
Theoretical Biophysics group at the University of Illinois, 16 Surles. M.C., Richardson, J.S., Richardson, D.C., and
who have been tremendously helpful in making suggestions Brooks. F.P. Sculpting proteins intenlctively: Continual
and testing the program. This work is supported by grants energy minimnization embedded in a graphical mnodeling
from the National Institutes of Health (PHS 5 P41 system. Proteiu Sci. 1994, 3, 198-210
RR05969-04), the National Science Foundation (BIR- 17 Oesterheh, D. and Stoeckenius. W. Functions of a new'
9318159), and the Roy J. Carver Charitable Trust. photoreceptor mnemnbranc. Proc, NaIL Acad. Sci. U.S.A.
,-) ,~
1973, 70, ,853-_857
18 Pugliese. L., Coda. A., Malcovati, M., and Bolognesi,
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