FMD
Fast Molecular Dynamics
A Programmer's Guide
For FMD Version 1.11.5
17 March 2000
Document Maintained by James A. Lupo
Introduction
Computational Details
Force Field Details
Electrostatics
van der Waals
Bonded Exclusions
Switching Functions
Bonds
Angles
Dihedrals
Harmonic Constraints
Spherical Boundary Conditions
Integrating the Equation of Motion
Minimization
Langevin Dynamics
Velocity Rescaling
Units and Constants
Units
Constants
Conversion Factors
Program Design Considerations
Process Description
Decomposition
Communications per Time Step
Communication Example
Load Balance
Node Algorithm per Time Step
Node Process Design
Patch Structure
Force Object Interface
Full Electrostatics
Partitioning of Forces into Long- and Short-Range
FMM3D Summary
Internal Detail -- Neighborhoods and Interaction Lists
Design Decisions in FMM3D
Tricks in FMM3D
Choosing Parameter Values for FMM3D
Design Decisions
Nitty-Gritty
Source Tree Structure
Style Conventions
CVS Keywords
File Names
Header Files
Source Code Names
User Parameters
User Input File Syntax
Required User Parameters
Basic User Parameters
FMM3D User Parameters
Harmonic Constraint Parameters
Energy Minimization Parameters
Langevin Dynamics Parameters
Temperature Rescaling Parameters
Periodic Boundary Condition Parameters
Spherical Boundary Condition Parameters
Applied Electric Field Parameters
Equivalent X-PLOR Parameters
Development Parameters
HDF File Format
Implementation Details
Program Structure
Initialization
More ...
Global Definitions
Global Functions
Global defines
Global typedef's
Class Descriptions
AngleForce
BondForce
BoundaryMap
BufferMPI
Collect
Communicate
CommunicateMPI
ConfigList
ConstraintForce
DihedralForce
ElectForce
FieldForce
FMAInterface
FullDirect
GenericList
GlobalIntegrate
HashTable
ImproperForce
Integrate
Inform
IntList
IntTree
LintList
LoadBalance
LongForce
Message
MessageManager
MessageQueue
Molecule
MultiBond
NameTable
NeighborList
Node
Output
Parameters
ParseOptions
Patch
PatchDistrib
PatchList
PDB
PDBAtom, PDBAtomRecord, PDBHetatm
PDBData, PDBUnknown
RecBisection
SimParameters
SphericalBCForce
Timer
UnitCell
Vector
WildCard
Miscellaneous Items
Base 64
DCDlib
HDFlib
STRlib
Validation Tests
References
Variable/Constant Index
Function Index
Concept Index
This document was generated on 20 March 2000 using the
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