FMD
Fast Molecular Dynamics
A User's Guide
For FMD Release 1.11.5
17 March 2000
Document Maintained by James A. Lupo
Introduction
Overview
Execution
Molecular Data File Formats
PDB Files
HDF files
PSF Files
Parameter Files
DCD Trajectory Files
User Input File Format
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
Notes on Non-Bonded Interactions
van der Waals Interactions
Electrostatics
Pair List Generation
Example
Installation
Installation Overview
Installation Details
Autoconf configuration
Manual configuration
Regenerating Documentation from Sources
Utilities
fmd.ui.tcl
energies.awk
stripmine.pl
engdump
fmdarch
hdf2pdb
hdfdump
quanta2fmd
swap.awk
send-pr
Validation
References
Sample PSF File
Sample Parameter File
Variable Index
Concept Index
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