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This is
the user manual for people who want to work with an existing model type
and perform straightforward calculations. Less commonly used and
advanced procedures as well as how to implement a new model type, are
described in the Technical Documentation.
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INTRODUCTION
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Introduction: Getting Started. Which
modules and what files to use.
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Model Types
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How to
build and use models: [1] rrRNAv1,
coarse-grained models of RNA and associated proteins; [2] rrDNAv1, a multiscale DNA; [3] Emmental, a model for fitting into
density maps; [4] VirPack, packing
of DNA viruses.
The force field assembly section in
the Technical Documentation provides instructions on how to implement a
new model type.
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Molecular Simulation
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Molecular
simulation with the models built in the previous section. A user
oriented manual is not yet available, see the Technical Documentation for now.
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| PROGRAMS |
Fitting
molecular structures into density maps: Yup.scx |
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Defunct
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THE
TARO MODULE: The Taro module is
designed for interactive use and has more features than the Yammp
module. GRAPHICAL USER INTERFACE: Most functions are
accessible from the graphical user interface. The first thing the user
has to do is to define a molecular system, i.e., assemble a force field. THE YAMMP MODULE:
The
Yammp module is designed for
computationally intensive simulations in a non-interactive (batch)
environment. (This is the Yammp 1 version.)
GRAPHICAL SCRIPT BUILDER Scripter: A graphical application to
build scripts for the Yammp module. (This is the Yammp 1 version.)
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The
links above will bring you to sub-sections of the user manual. In
addition to the standard links to other sections, there will be links
to sub-sections.
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