Contents
Release 97.2, May 1998
Table of Contents
1. Introduction
- What is the Discover® program?
- What Discover can do
- Comparison of C and FORTRAN versions
- CDiscover--Cerius2, Insight and standalone modes
- Accessing CDiscover
- How to use the documentation
- Electronic information sources
- Typographical conventions and terminology
2. CDiscover within Cerius2
- Preparing the model and forcefield
- Choosing the forcefield
- Building or loading models
- Assigning atom types and charges
- Defining charge groups
- Setting constraints
- Fixed atoms
- Constraints during dynamics
- Preparing the energy expression
- Nonbond interactions
- Parameter scaling
- What to do if some parameters cannot be assigned
- Setting up the simulation conditions
- Single-point energy and gradient calculations
- Minimization
- Specifying the minimization algorithm
- Setting convergence criteria
- Maximum number of iterations
- Dynamics
- Defining the timestep
- Defining the thermodynamic ensembles
- Controlling temperature, pressure, and stress
- Type of dynamics simulation
- Stages of a dynamics run
- Setting up and starting the run
- Specifying output
- Specifying how and where to send the job
- Interactive vs. background or NQS run mode
- Selecting a machine and base directory
- Setting up NQS-mode jobs
- Monitoring and controlling running jobs
- Transferring files from one machine to another
- Other file-control issues
- Starting the run
- Analyzing results
- Preparing trajectories
- Loading or creating a trajectory
- Selecting frames from a loaded trajectory
- Output from analysis
- Displaying model conformations
- Output as graphs and text
- Output in tables format
- Property statistics
- Basic statistics of various properties
- Mean-square displacement
- Self-diffusion constant
- Velocity autocorrelation
- Power spectrum
- Radial distribution function
- Structure factor
- Dipole-dipole interactions
- Fluctuation analysis
3. CDiscover within Insight
- General procedure
- Setting up the ESFF forcefield
- CDiscover background jobs
- Using the Background_Job pulldown
- Setting up a background job
- Interactive screen coordinate updates
- Examining completion status
- Killing a background job
- In case of run errors
- Tutorial--The Insight Environment
- Pilot online tutorials
- Tutorials in hypertext format
- Overview of tutorial lessons
- Lesson 5: Generating a phi/psi map
- Command Summary--The Insight Environment
- Setup pulldown
- Strategy pulldown
- Specify pulldown
- Calculate pulldown
- Language_Control pulldown
- Analyze pulldown
- Pseudo_Atom pulldown
- Background_Job pulldown
- D_Run pulldown
4. Standalone CDiscover
- Input files required
- Overview of BTCL commands
- Calculation commands
- Commands for calculation setup and analysis
- Input commands
- Output commands
- Control commands
- Exiting a BTCL session
- Defining and using your own procedures
- Performance and convenience
- Databases
- Objects
- Initiating a run
- Direct method
- Using the interactive utility
- File redirection method
- Running CDiscover in parallel
- Scripts and program initialization
- An example CDiscover run
- Input files
- Explanation of command input file
- Initiating the run
- History file support
- Editing the ESFF forcefield parameters
- Tutorial--Standalone Mode
- Overview of tutorial lesson
- Lesson 1: Using BTCL and TCL commands to manipulate the geometry of two helices
- Command Summary--Standalone Mode
APPENDICES
A. Btcl Language and Commands--Standalone Mode
- MSI (Biosym) Tcl language syntax
- General programming syntax
- Variables and expressions
- Special characters and the expr and eval commands
- Control statements
- Conditional statements: if, else, and elseif
- Conditional looping statements: while, for, and foreach
- Btcl procedures
- Btcl commands and utilities
- Btcl command parameter types
- Global Btcl and Tcl variables and environment variables
- Exiting a Btcl session
- Conventions in documentation of Btcl commands
- Font conventions for keywords
- Assignment and types of values
- Punctuation conventions
- Command descriptions
- analyzeNonbond
- atomMovability
- begin
- cellParameter
- database
- $dbHandle
- diffraction
- discoverHistory
- dynamics
- energy
- energyContribution
- forcefield
- geometry
- help
- minimize
- molGeom
- object
- output
- peek
- print
- pseudoAtom
- rattle
- readFile
- reset
- restraint
- select
- subset
- subStructure
- vdWTailCorrection
- vector
- vibrationalAnalysis
- writeFile
B. Databases and Tables
- Introduction to databases and tables
- Introduction
- Illustrations
- Data types for columns
- System database
- Introduction
- Contents of the system database common to all systems
- Atom table
- Monomer table
- Molecule table
- NonbondGroup Table
- Bond table
- Contents of the system database for periodic systems
- Introduction to symmetry and periodicity
- Differences from simple systems
- Descriptions of new and augmented tables
- Contents of the system database for systems with symmetry and periodicity
- Differences from simpler systems
- Descriptions of new and augmented tables
- Subset tables
- PseudoAtom table
- Internal energy exclusion
- Nonbond energy exclusion
- Consensus dynamics
- Energy database
- Introduction
- Contents of the energy database
- Values table
- Atom table
- Accessing the energy database
- Minimize database
- Dynamics database
- Miscellaneous examples
C. Discover Interprocess Communication (IPC)
- Purpose
- Background
- IPC components
- Discover Btcl IPC commands
- MSI IPC client application program interface
- ipc procedure
- Common IPC operations
- Advanced IPC operations
- Common IPC operations
- init
- Advanced IPC operations
- accept
- connect
- eval
- listen
- poll
- send
- server
- Interprocess communication for Discover--discoverIO
- discoverIpc
- eval
- poll
- connect
- listen
- accept
- MSI IPC C application program interface
- Background
- C functions for IPC
- BiosymIpc_Init
- BiosymIpc_Shutdown
- BiosymIpc_Read
- BiosymIpc_Write
- BiosymIpc_Print
- BiosymIpc_VarWrite
- BiosymIpc_WriteRawBtcl2
- BiosymIpc_WriteRawBtcl
- BiosymIpc_SetChannel
- BiosymIpc_GetError
- BiosymIpc_GetLocalVersion
- BiosymIpc_GetRemoteVersion
- MSI IPC FORTRAN application program interface
- Background
- Subroutines
- BiosymIpc_Initf
- BiosymIpc_ReadHeaderf
- BiosymIpc_ReadString128f
- BiosymIpc_WriteIntegerf
- BiosymIpc_WriteReal8f
- BiosymIpc_WriteStringf
- BiosymIpc_WriteString128f
- BiosymIpc_WriteBtcl128f
- BiosymIpc_WriteRawBtcl128f
- BiosymIpc_GetErrorf
- BiosymIpc_GetLocalVersionf
- BiosymIpc_GetRemoteVersionf
- BiosymIpc_Int2Charf
- BiosymIpc_Char2Intf
- BiosymIpc_ReadIntegerf
- BiosymIpc_ReadReal8f
- BiosymIpc_ReadStringf
- MSI IPC C language structures
- Background
- IPC frames
D. Files
- Introduction
- Command input file (.inp)
- Sample CDiscover .inp file
- Forcefield parameter file (.frc)
- Format of .frc file
- Version and reference numbers
- MSI file identification
- Forcefield version
- Atom types
- Equivalence table
- Hydrogen bond donors and acceptors
- Quadratic bond-stretching potential
- Quartic bond-stretching potential
- Morse bond-stretching potential
- Quadratic angle-bending potential
- Quartic angle-bending potential
- Quadratic bond-bond interaction potential
- Quadratic bond-angle interaction potential
- One-term torsion potential
- Three-term torsion potential
- Four-term torsion potential
- Angle-angle-torsion interaction potential
- Peripheral bond-torsion interaction potential
- Central bond-torsion interaction potential
- Three-term angle-torsion interaction potential
- Out-of-plane potential, improper torsion definition
- Out-of-plane, Wilson definition
- Out-of-plane interaction potential using improper torsion definition
- Angle-angle interaction potential
- 6-9 Nonbond (van der Waals) potential
- 6-12 Nonbond (van der Waals) potential
- 10-12 Hydrogen bond potential
- Bond increments
- Standard output file (.out)
- CDiscover output files (.arc, .xfrc, .out, .tbl, .xdyn, user-named)
- Discover dynamics restart files (.xdyn)
- Automatic potential parameter assignment
- ESFF structure output file (.esf)
- ESFF forcefield parameter file (.epa)
- Torsion information
- Dynamics tabular output for energies (.gre)
- Dynamics tabular output for thermodynamic states (.grp)
- Dynamics scratch file (.pre)
INDICES
List of Tables
Tcl man pages
General Index
Last updated January 8, 1998.
Copyright © 1997, 1998, Molecular Simulations, Inc. All rights
reserved.