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Contents
Contents
MDynaMix Package
version 5.2.5
User manual
Alexander Lyubartsev
Division of Physical Chemistry
Stockholm University
13 March 2013
Contents
Introduction
Changes from previous versions
Description of the molecular structure and the force field
The force field
Molecular geometry and non-bonded interaction parameters
Bonds
Covalent angles
Dihedral angles
Optional features of the force field
The main input file
General notes
Basic setup
Restart control
System
Ensemble
Molecular Dynamics
Startup
Expanded Ensemble mode
Path Integral mode
Properties
Compilation
Sequential execution
Parallel execution
Other makefiles
Execution
Files used by the program
Memory considerations
Program structure
Makemol
utility
General organization
The force field (.ff) file
The molecular structure (.smol) file
Tranal
utility
General organization
tranal_base: reading trajectories
Computation of the electron density and electrostatic potential in bilayers: bileldens.f
Dielectric constant: diel.f
Diffusion: diffus.f
Dryrun: dryrun.f
Lateral diffusion: latdiff.f
Order parameters: order.f
Radial distribution functions: rdf.f
Spatial distribution functions: sdf.f
Distribution of torsion angles: torsion.f
Ramachandran plot for a pair of torsion angles: torsion2.f
Residence time calculation: restime.f
Time correlation functions: trtcf.f
About this document ...
Alexander Lyubartsev 2013-04-30
