The Discover Program - Index of topics

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A
• Algorithms, see dynamics, minimization, or nonbond cutoffs
• Atom specification

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  B

• biosym_tutorial script
• BTCL Language & Commands
  • Arithmetic operators
  • Array parameters
  • Basic concepts, short review for a tutorial
  • Boolean parameters
  • Brief introduction
  • Command input files, annotated examples - see tutorials
  • Command & utilities in statements (general syntax)
  • Commands listed alphabetically
  • Commands listed by function
  • Commands overview
  • Conditional statements
  • Control statements
  • Databases
  • Documentation of the syntax
  • Ending a BTCL session
  • Enumerated parameters
  • Environment variables
  • expr & eval commands
  • Expressions & variables
  • File-identification variable
  • Format for documenting syntax
  • Functions available
  • Global variables
  • ``How-to'' index
  • if statements
  • Integer parameters
  • Ipc commands
  • Logical operators
  • Looping statements
  • Mathematical operators
  • Operators in expressions
  • Overview of commands
  • Procedures
  • PROJECT variable
  • Random number generator
  • randomSeed variable
  • Real parameters
  • Reserved characters
  • Returning values
  • Special characters
  • String parameters
  • Subcommands within command statements
  • Tutorial lessons
  • Types of parameters
  • User-defined procedures
  • Utilities
  • Variables & expressions
• Buckingham nonbond interaction potential
• Bulk solvent

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  C

• Cartesian vs crystal axes
• Cell parameters, finding and changing
• Cell multipole method
  • BTCL forcefield command
• Citations
• Communicating with other programs
• Constraints and restraints
  • BTCL rattle command
  • RATTLE implementation and test results
  • BTCL restraint command
• Crystal vs Cartesian axes
• Crystals

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  D

• Databases (internal to the Discover program)
  • Dynamics
  • Energy
  • Minimize
  • System
  • Using databases:
    • Excluding specific atoms from a calculation
    • Excluding certain nonbond interactons from an energy calculation
• Describing the system
• Dielectric constant
  • BTCL forcefield command
  • Dielectric in AMBER
• Dynamics
  • ABM4 integrator
  • Algorithms
  • Algorithms, results compared
  • Andersen method
  • Background
  • Berendsen method of pressure control
  • Berendsen method of temperature-bath coupling
  • BTCL dynamics command
  • Canonical ensemble
  • Colliding hydrogens example
  • Conformational search of ANF
  • Conformational space
  • Consensus dynamics
  • Constant-energy, constant volume ensemble
  • Constant-pressure, constant enthalpy ensemble
  • Constant-temperature, constant-pressure ensemble
  • Constant-temperature, constant-stress ensemble
  • Constant-temperature, constant-volume ensemble
  • Data-collection stage of run
  • Direct velocity scaling
  • Equilibration stage of run
  • Example calculations
  • General methodology
  • Integration algorithms
  • Integration errors
  • Introduction
  • Major uses of molecular dynamics
  • Microcanonical ensemble
  • Nosé
  • NPH ensemble
  • NPT ensemble
  • NST ensemble
  • NVE ensemble
  • NVT ensemble
  • Parrinello-Rahman method of pressure & stress control
  • Pressure & stress
  • Restarting a run
  • Run duration
  • Runge-Kutta-4 integrator
  • Statistical ensembles
  • Stress & pressure
  • Temperature
  • Temperature-bath coupling
  • Thermodynamic ensembles
  • Timestep length
  • Tutorial, Insight interface
  • Tutorial, constant-stress, Insight interface
  • Tutorial, restarting dynamics, Insight interface
  • Vasopressin example
  • Velocity scaling
  • Verlet leapfrog integrator
  • Verlet velocity integrator

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  E

• Empirical fit of the potential energy surface
• The energy expression
• Environment variables
• Ewald summation technique
  • BTCL forcefield command
• Example BTCL statements
  • Minimization with specified algorithm(s)
  • Finding all atoms that are attached to certain atoms
  • Finding and setting a specified angle in all monomers of a given type
  • Assigning (defining, setting up) geometric objects
  • Use atom-based method to make nonbond summation list
  • Obtaining atomic coordinates
  • Reading a binary forcefield file
  • Writing a binary forcefield file
  • Changing defaults for dynamics
  • Restraining a torsion to cis conformation
  • Combining (concatenating) geometric objects
  • Consensus dynamics
  • Constant-stress/constant-temperature dynamics
  • Listing the contents of a subset
  • Listing the contents of a subset, for filtering or error-trapping
  • Constraining angles during dynamics
  • Constraining all bonds to current lengths during dynamics
  • Constraining bonds to specified lengths during dynamics
  • Changing the convergence criteria for minimization
  • Reading coordinate and molecular data files
  • Writing coordinate and molecular data files
  • Reading a coordinate file
  • Writing a coordinate file
  • Database of databases
  • Decomposition of internal energy
  • Using default molecular data and forcefield files
  • Defining pseudoatoms and finding their coordinates
  • Defining pseudoatoms from subsets
  • Setting the diagonal of a matrix
  • Diagonalizing a vector
  • Finding a dihedral angle
  • Reading a dynamics restart file
  • Writing a dynamics restart file
  • Calculating dipole moments
  • Creating a table of dipole moments from sets of coordinates in an archive file
  • Disable automatic forcefield parameters
  • Displacing (moving) the positions (coordinates) of one atom in all monomers of a given type
  • Display all warning messages
  • Finding distance between geometric objects (points, lines, etc.)
  • Finding distances between objects containing different numbers of atoms
  • Changing a certain interatomic distance in all monomers of a given type
  • Dynamics under default conditions
  • Finding eigenvectors
  • Electron diffraction curve
  • Requesting printout of energy values
  • Excluding the internal energy calculation for certain atoms
  • Extracting an element from a matrix
  • Fixed (frozen) pseudoatoms
  • Using Fixed-geometry water molecules during dynamics
  • Fixing (freezing) atom positions
  • Reading all frames from an archive file
  • Reading one frame from a history file
  • Writing one frame to an archive file
  • Getting (retrieving, finding) geometric information
  • Global database information
  • Writing a Hessian file
  • Accessing & manipulating the Hessian matrix
  • Finding a least-squares line
  • Line geometric objects, assigning
  • Listing information on pseudoatoms
  • Mass-weighted pseudoatoms
  • Changing a matrix into a vector
  • Minimization under default conditions
  • Monitoring progress of dynamics run
  • Monitoring progress of minimization run
  • Finding all monomer types in a molecule
  • Moving (translating) geometric objects in space
  • Working with multiple molecular systems
  • Nonbond interactions between sets (databases) of atoms
  • Specifying a non-default forcefield
  • Normal mode analysis
  • Output electrostatic energy periodically during minimization
  • Parrinello method in dynamics
  • Point geometric objects, assigning
  • Using precedence rules in selecting atoms
  • Printing during a minimization run
  • Printing multiple tables for a dynamics run
  • Creating a quadratic distance restraint
  • Creating a quadratic and relative angle restraints
  • Creating a relative distance restraint
  • Removing a system from consideration
  • Report any monomers not containing a given atom
  • Restarting dynamics
  • Resetting the startup files
  • Making an rms comparison of the atomic coordinates of two monomers
  • Finding an rms residual
  • Rotating (changind) a dihedral angle
  • Joining scalar & vector objects
  • Scale certain forcefield terms
  • Scale nonbond terms in AMBER forcefield
  • Direct scaling of a bond length
  • Scattering angles
  • Listing selected atoms in certain monomers
  • Selecting alpha-carbons of certain monomers
  • Selecting all monomers except a certain type
  • Selecting atoms in periodic systems
  • Selecting atoms in symmetric systems
  • Selecting only certain monomers
  • Selecting groups using tables and databases
  • Separate nonbond lists for van der Waals & Coulombic interactions
  • Selecting a specific forcefield from a forcefield file
  • Defining a subset containing all defined subsets in a molecule
  • Defining a subset containing all defined subsets in a system
  • Defining subsets consisting of all hydrogens in each monomer of a molecule
  • Defining subsets consisting of all monomers in a molecule
  • Defining subsets containing certain angles , using a table in a database
  • Defining subsets containing certain angles , in a slightly different way
  • Indicating atoms in symmetry groups
  • Systematic conformational search
  • Creating tables in databases
  • Transformation matrices
  • Updating the coordinates of pseudoatoms after positions of their component atoms have changed
  • Creating a user-defined restraint
  • User-specified weights in defining pseudoatoms
  • Changing a vector into a matrix
  • Creating & manipulating vectors
  • Using vector variables in procedures & functions
  • Vibrational analysis with output of Hessian file
  • Vibrational analysis with output to vector and matrix
  • Calculating vibrational frequencies under default conditions
  • X-ray scattering pattern
• Explicit-image model

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  F

• Files, annotated examples - see tutorials
• Forcefields
  • AMBER
  • AMBER for carbohydrates
  • AMBER 1-4 scale terms
  • Assignment of atom types
  • Atom type equivalences
  • Automatic forcefield
  • BTCL begin command
  • BTCL forcefield command
  • CFF91
  • Consistent forcefield
  • Consistent valence forcefield
  • CVFF
  • Definition
  • Dielectric in AMBER
  • in Discover
  • The energy expression
  • ESFF
  • Extensible systematic forcefield
  • General introduction & descriptions
  • Homans' Carbohydrate Forcefield
  • Missing parameters
  • Parameter association with atom types
  • Quality of
  • Specifying which forcefield
  • The target function
  • What they are
  • Wildcard atom types

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  G

• Geometry manipulation tutorial, BTCL commands (butane)
• Geometry manipulation tutorial, BTCL commands (helix)
• Gifts
• Global variables
• Graphics

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  H

• Manipulating dynamics history information
• HTML browser

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  I

• non-standard IEEE representation
• Input files, annotated examples - see tutorials
• Interprocess communication
• Introduction to User Guide
• Ipc commands

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  J

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  K

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  L

• Literature

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  M

• Mosaic
  • Additional information
  • Basic navigation
  • CERN, resources at
  • Configuring
  • Ease-of-use
  • Font
  • Interrupting a connection
  • Installing
  • Keyboard shortcuts
  • Links
  • Menus & buttons
  • NCSA, resources at
  • Page size
  • Printer
  • Obtaining
  • Setting up
  • Using
  • Viewing graphics
  • X-defaults
• Minimization
  • Algorithms
  • Algorithms, how to choose
  • BTCL minimize command
  • Conjugate gradients
  • Constraints & restraints, when to use
  • Convergence criteria
  • DHFR-trimethoprim binding study
  • Example calculation
  • General methodology
  • Introduction
  • Iterative Newton-Raphson method
  • Line searches
  • Minimum-energy structure, significance of
  • Newton-Raphson methods
  • Quasi Newton-Raphson method
  • Simple example
  • Steepest descents
  • Truncated Newton-Raphson method
  • Tutorial, Insight interface
  • Vibrational calculations
• Molecular dynamics

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  N

• Nonbond interactions, calculations of
  • BTCL forcefield command
  • Cell multipole method
  • Cutoffs
  • Ewald summation technique
  • Periodic systems
  • Scaling in AMBER
  • System size, effect of
• Nonbond cutoffs
  • Algorithm
  • BTCL forcefield command
  • Charge groups
  • Coulombic interactions
  • Neighbor list
  • Reason for using
  • System size, effect of
  • van der Waals interactions
  • Variable names

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  O

• Objects, BTCL
• Output files, annotated examples - see tutorials

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  P

• Periodic boundary conditions
• Pictures
• The potential energy surface
• precision
• PROJECT variable
• Pseudoatoms and their use

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  Q

• Quartic form for van der Waals term

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  R

• Random number seed
• References
• Restraints and constraints
  • BTCL rattle command
  • BTCL restraint command
• Specifying the run name

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  S

• Schrödinger equation

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  T

• Tables
  • Introduction to the concept
  • See also Databases
• Tethering
• Template forcing
• Thermodynamics
• TCL and TK (site at www.sco.com)
• TCL man pages
• Transition states
• Tutorials
  • biosym_tutorial script
  • BTCL commands
  • Constant-stress dynamics, Insight interface
  • Diffusion of water
  • Discover_3 module
  • Dynamics, Insight interface
  • Geometry manipulation, BTCL commands (butane)
  • Geometry manipulation, BTCL commands (helix)
  • Insight interface
  • Minimization, Insight interface
  • Restarting dynamics, Insight interface
  • Setting up
  • Standalone mode
  • Using a pre-recorded BTCL script in the Discover_3 module
  • Hints & guidance for writing your own BTCL scripts

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  U

• Units used
• User Guide, overview

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  V

• Vibrational calculations
  • BTCL vibrationalAnalysis command
  • Example calculation
  • Frequencies
  • General methodology
  • Minimization and

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  W

• The World-Wide Web
  • CERN, resources at
  • Chemistry resources
  • NCSA, resources at
  • Other resources

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  X

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  Y

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  Z

Main access page

Other access