Contents
Release 2000, March 2000
Contents
1. Introduction
- What Is the Discover® program?
- The FDiscover program--the Insight and standalone modes of operation
- Comparison of FDiscover and CDiscover
- Starting the FDiscover program
- Using this guide
- Additional information
- Note on documentation of command names
- The Insight mode of running the FDiscover program
- Standalone mode of the FDiscover program
2. Application--The Insight Environment
- Command summary
- Outline of using FDiscover within Insight
- Methodology
- Setting up the calculation
- Types of calculations
- Minimization
- Dynamics
- Using constraints and restraints
- Other parameters
- Analyzing the results
3. Application--Standalone Version
- User interface
- Input files required for the Discover program
- The Discover command input file (.inp)
- The Cartesian coordinate and molecular data files (.car and .mdf files)
- Selecting a forcefield file (.frc/.bin)
- Submitting the Discover job
- Job status
- Output files produced by the Discover program
- Methodology
- Step 1: Setting up the energy
- Step 2: Types of calculations
- Minimization
- Molecular dynamics
- Free energy calculations
- Analysis of results
- Miscellaneous commands
- Discover Simulation Language (DSL)
4. Tutorial
- Pilot online tutorials
- Overview of tutorial lessons
- Lesson 1: Minimizing and performing molecular dynamics
- Lesson 2: Relative free energy
- Lesson 3: Using pseudoatoms
- Lesson 4: Consensus dynamics/minimization
- Lesson 5: Minimizing the magainin peptide--standalone mode
- Lesson 6: Conformational search by high-temperature dynamics--standalone mode
APPENDICES
A. Commands and DSL--Standalone Mode
- Discover Simulation Language syntax
- Procedure command statement
- Arithmetic replacement statement
- Logical if statement
- Unconditional goto statement
- Print using statement
- Format statement
- Comment statement
- Continuation statement
- End statement
- Syntax checking
- Command documentation format
- Command descriptions
- archive
- assign angle name
- assign atom pair name
- assign torsion name
- begin
- calculate absolute
- calculate relative
- comparison list generation
- constrain
- define average atom
- enclose
- fix
- fixed atom list generation
- force
- initialize
- interaction
- intermolecular interaction
- log
- minimize
- print
- pull
- randomize coordinates
- read
- reduce output
- restart dynamics
- restrain
- resume dynamics
- retrieve
- rms
- rotors
- scale
- set
- tabulate
- template force
- tethered atom list generation
- vibrational
- warp
- Parameters accessible from DSL
- Parameters affecting minimization
- Atom overlap
- Movement limit
- Precision of line minimization
- Conjugate gradient formula
- Parameters affecting dynamics
- Temperature control via direct velocity scaling
- Temperature control via coupling to a temperature bath
- Temperature initialization
- Pressure control via coupling to a pressure bath
- Miscellaneous
- Parameters controlling forcefields
- Nonbond energy cutoff parameters
- Template forcing
- Miscellaneous
- Parameters controlling periodic boundary conditions
- Parameters controlling restraints
- Parameters controlling electric field calculations
- Parameters affecting parallel running of the FDiscover program
B. Files
- Introduction
- Command input file (.inp)
- Sample FDiscover .inp File
- Forcefield parameter file (.frc)
- Molecular template file (.tem)
- Standard output file (.out)
- Discover dynamics restart files (.ors and .rst)
- Log file (.ref)
- Progress report file (.pek)
- Automatic potential parameter assignment file (.prm)
- Torsion file (.tor)
- Dynamics tabular output for energies (.gre)
- Dynamics tabular output for thermodynamic states (.grp)
- Dynamics scratch file (.pre)
- Vibrational frequencies and eigenvectors (.frq)
- Internal coordinate eigenvectors (.nmo)
- Warped parameter output file (.wrp)
- Free energy running averages table (.tot)
- Comparison list file (.cli)
- Free energy scratch file (.xxx)
- Relative free energy table for convergence plots (.tbl)
C. Utilities
- Discover utilities
- binff
- dirtoseq
- formhis
- seqtodir
- uformhis
List of Figures
List of Tables
Index
Last updated March 8, 2000.
Copyright © 2000, Molecular Simulations, Inc. All rights
reserved.