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Table Of Contents

1. Introduction
1.1. What to read next
1.2. Information flow in Amber
1.2.1. Preparatory programs
1.2.2. Simulation programs
1.2.3. Analysis programs
1.3. Installation of Amber 10
1.3.1. More information on parallel machines or clusters
1.3.2. Installing Non-Standard Features
1.3.3. Installing on Microsoft Windows
1.3.4. Testing
1.3.5. Memory Requirements
1.4. Basic tutorials
2. Sander basics
2.1. Introduction
2.2. Credits
2.3. File usage
2.4. Example input files
2.5. Overview of the information in the input file
2.6. General minimization and dynamics parameters
2.6.1. General flags describing the calculation
2.6.2. Nature and format of the input
2.6.3. Nature and format of the output
2.6.4. Frozen or restrained atoms
2.6.5. Energy minimization
2.6.6. Molecular dynamics
2.6.7. Self-Guided Langevin dynamics
2.6.8. Temperature regulation
2.6.9. Pressure regulation
2.6.10. SHAKE bond length constraints
2.6.11. Water cap
2.6.12. NMR refinement options
2.7. Potential function parameters
2.7.1. Generic parameters
2.7.2. Particle Mesh Ewald
2.7.3. Using IPS for the calculation of nonbonded interactions
2.7.4. Extra point options
2.7.5. Polarizable potentials
2.7.6. Dipole Printing
2.7.7. Detailed MPI Timings
2.8. Varying conditions
2.9. File redirection commands
2.10. Getting debugging information
3. Force field modifications
3.1. The Generalized Born/Surface Area Model
3.1.1. GB/SA input parameters
3.1.2. ALPB (Analytical Linearized Poisson-Boltzmann)
3.2. Poisson-Boltzmann calculations
3.2.1. Introduction
3.2.2. Usage and keywords
3.2.3. Example inputs
3.3. Empirical Valence Bond
3.3.1. Introduction
3.3.2. General usage description
3.3.3. Biased sampling
3.3.4. Quantization of nuclear degrees of freedom
3.3.5. Distributed Gaussian EVB
3.3.6. EVB input variables and interdependencies
3.4. Using the AMOEBA force field
3.5. QM/MM calculations
3.5.1. The hybrid QM/MM potential
3.5.6. General QM/MM &qmmm Namelist Variables
3.5.7. Link Atom Specific QM/MM &qmmm Namelist Variables
4. Sampling and free energies
4.1. Thermodynamic integration
4.1.1. Basic inputs for thermodynamic integration
4.1.2. Softcore Potentials in Thermodynamic Integration
4.2. Umbrella sampling
4.3. Targeted MD
4.4. Steered Molecular Dynamics (SMD) and the Jarzynski Relationship
4.4.1. Background
4.4.2. Implementation and usage
4.5. Replica Exchange Molecular Dynamics (REMD)
4.5.1. Changes to REMD in Amber 10
4.5.2. Running REMD simulations
4.5.3. Restarting REMD simulations
4.5.4. Content of the output files
4.5.5. Major changes from sander when using replica exchange
4.5.6. Cautions when using replica exchange
4.5.7. Replica exchange example
4.5.8. Replica exchange using a hybrid solvent model
4.5.9. Changes to hybrid REMD in Amber 10
4.5.10. Cautions for hybrid solvent replica exchange
4.5.11. Reservoir REMD
4.6. Adaptively biased MD, steered MD, and umbrella sampling with REMD
4.6.1. Overview
4.6.2. Reaction Coordinates
4.6.3. Steered Molecular Dynamics
4.6.4. Umbrella sampling
4.6.5. Adaptively Biased Molecular Dynamics
4.7. Nudged elastic band calculations
4.7.1. Background
4.7.2. Preparing input files for NEB
4.7.3. Input Variables
4.8. Constant pH calculations
4.8.1. Background
4.8.2. Preparing a system for constant pH
4.8.3. Running at constant pH
4.8.4. Analyzing constant pH simulations
4.8.5. Extending constant pH to additional titratable groups
4.9. Low-MODe (LMOD) methods
4.9.1. LMOD conformational searching and flexible docking
4.9.2. LMOD Procedure
4.9.3. XMIN
4.9.4. LMOD
4.9.5. Tricks of the trade of running LMOD searches
5. Quantum dynamics
5.1. Path-Integral Molecular Dynamics
5.1.1. General theory
5.1.2. How PIMD works in Amber
5.2. Centroid Molecular Dynamics (CMD)
5.2.1. Implementation and input/output files
5.2.2. Examples
5.3. Ring Polymer Molecular Dynamics (RPMD)
5.3.1. Input parameters
5.3.2. Examples
5.4. Reactive Dynamics
5.4.1. Path integral quantum transition state theory
5.4.2. Quantum Instanton
5.5. Isotope effects
5.5.1. Thermodynamic integration with respect to mass
5.5.2. AMBER implementation
5.5.3. Equilibrium isotope effects
5.5.4. Kinetic isotope effects
5.5.5. Estimating the kinetic isotope effect using EVB/LES-PIMD
6. NMR and X-ray refinement using SANDER
6.1. Distance, angle and torsional restraints
6.1.1. Variables in the &rst namelist:
6.2. NOESY volume restraints
6.3. Chemical shift restraints
6.4. Pseudocontact shift restraints
6.5. Direct dipolar coupling restraints
6.6. Residual CSA or pseudo-CSA restraints
6.7. Preparing restraint files for Sander
6.7.1. Preparing distance restraints: makeDIST_RST
6.9. Time-averaged restraints
6.10. Multiple copies refinement using LES
6.11. Some sample input files
6.11.1. 1. Simulated annealing NMR refinement
6.11.2. Part of the RST.f file referred to above
6.11.3. 3. Sample NOESY intensity input file
6.11.4. Residual dipolar restraints, prepared by makeDIP_RST:
6.11.5. A more complicated constraint
7.3. PMEMD-specific namelist variables
7.4. Slightly changed functionality
7.5. Parallel performance tuning and hints
7.6. Installation
7.7. Acknowledgements
8.1. General instructions
8.2. Input explanations
8.2.1. General
8.2.2. Energy Decomposition Parameters
8.2.3. Poisson-Boltzmann Parameters
8.2.4. Molecular Mechanics Parameters
8.2.5. Generalized Born Parameters
8.2.6. Molsurf Parameters
8.2.7. NMODE Parameters
8.2.8. Parameters for Snapshot Generation
8.2.9. Parameters for Alanine Scanning
8.2.10. Trajectory Specification
8.3. Preparing the input file
8.4. Auxiliary programs used by MM_PBSA
8.5. APBS as an alternate PB solver in Sander
9. LES
9.1. Preparing to use LES with AMBER
9.2. Using the ADDLES program
9.3. More information on the ADDLES commands and options
9.3. More information on the ADDLES commands and options
9.4. Using the new topology/coordinate files with SANDER
9.5. Using LES with the Generalized Born solvation model
9.6. Case studies: Examples of application of LES
9.6.1. Enhanced sampling for individual functional groups: Glucose
9.6.3. Improving conformational sampling in a small peptide
10. Divcon
10.1. Introduction
10.2. Getting Started
10.2.1. Standard Jobs
10.2.2. Divide and Conquer Jobs
10.3. Keywords
10.3.1. Hamiltonians
10.3.2. Convergence Criterion
10.3.3. Restrained Atoms
10.3.4. Output
10.3.5. General
10.3.6. Gradient
10.3.7. Atomic Charges
10.3.8. Subsetting
10.4. Solvation
10.5. Nuclear Magnetic Resonance(NMR)
10.5.1. Default Keywords
10.6. Citation Information
11. Miscellaneous
11.1. ambpdb
11.2. protonate
11.3. ambmask
11.4. pol_h and gwh
11.5. fantasian
11.6. elsize
A. Namelist Input Syntax
B. GROUP Specification
C. EVB output file specifications
D. Distributed Gaussian EVB format specifications
D.1. Cartesian coordinate representation
D.2. Internal coordinate representation
E. AMBER Trajectory NetCDF Format
E.1. Introduction
E.2. Program behavior
E.3. NetCDF file encoding
E.4. Global attributes
E.5. Dimensions
E.6. Variables
E.6.1. Label variables
E.6.2. Data variables
E.7. Example
E.8. Extensions and modifications
E.9. Revision history
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Published by: David Nei on Nov 11, 2010
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