User Manual

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.

INTRODUCTION

Introduction: Getting Started. Which modules and what files to use.

Model Types

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.

Molecular Simulation

Molecular simulation with the models built in the previous section. A user oriented manual is not yet available, see the Technical Documentation for now.

PROGRAMS Fitting molecular structures into density maps: Yup.scx

Defunct

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.)

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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