YUP Tutorial Module 0: Preparations

1. Introduction

YUP or Yammp 2 is a general-purpose molecular mechanics program. It is particularly well suited for simulations of reduced representation models. Reduced or simplified models are those that do not represent molecules in all-atom details. Simplified models enable much larger molecular systems to be studied at the price of lower resolution and a coarser level of details. YUP is written as an extension of the general purpose programming language Python. In turn, the language serves for model building and user scripting. A large part of YUP itself is written in Python; the computationally intensive parts have been written in C and compiled to machine code.
Sections

1. Introduction
2. Python
3. Objects
4. Exercises

Requirements

You are assumed to have the following skills:

1 Basic familiarity with the UNIX command line environment. Any variety of UNIX will do (BSD, LINUX, etc)
2 Some programming experience, particularly in a modern language.
3 Text editing.
4 Spreadsheet and graphing applications.

Modules

This is Module 0 of a six module tutorial. This module deals with preparations for the actual tutorial. Complete all four chapters of this module before you come to the Workshop. All you need is a reasonably up-to-date Python interpreter; which you should find on LINUX and MacOS X machines. You need to learn some Python (Chapter 2) before you can use YUP. If you wish to complete Module 3, make sure you are comfortable with Python and object-oriented programming; Chapter 4 is a programming exercise that might help. We will go over this exercise at the Workshop if there is a need.

For Module 1 onwards, you can attend a Yammp Workshop or you can download and install the YUP package to work through the exercises yourself. Two platforms are supported at this time: [1] x86 LINUX and [2] PowerPC MacOS X. The earliest Python interpreter that you can use is at least version 2.2. It would also be helpful to have the X11 environment, a Python-aware text editor, a spreadsheet and graphing program, and a web browser.

In Module 1, you will learn to build simplified DNA models and carry out molecular mechanics simulations.

Module 2 brings you on a tour of the internal data structures of YUP to prepare you for the next module.

In Module 3, you will learn to write scripts to automate simulations and programs to carry out novel calculations. You will also learn how to assemble the force field for a simple molecular model. This is for advanced users who wish to carry out complex calculations.

Module 4 is a discussion of the force field assembly process. There are no exercises, but you are directed to examine code.

The following modules are not yet ready: Module 5 covers the development of new force field terms. Module 6 is an exercise in multi-scale modeling using the simplified DNA (rrDNAv1) model. Module 7 is a tutorial for the reduced representation RNA (rrRNAv1) model.

Study Plan

If you are interested in: Complete Modules Optional Modules and Chapters
1. Implementing a new model type 0 to 4 Modules 6 and 7
2. Using the rrDNAv1 model 0 to 2 and 6 Chapter 4 of Module 0
3. Using the rrRNAv1 model 0 to 2 and 7 Chapter 4 of Module 0
4. Implementing a new force field term 0 to 5 Modules 6 and 7

Modules

0. Preparations
1. Model Construction and Simulations
2. Programming with YUP Part 1
3. Programming with YUP Part 2
 4. Force field Assembly
5. Developing Potential Energy Terms

For the Harvey Lab. only

Only the dual-processor G4 Power Macintoshes and all G5 models have all the necessary software to run YUP. Make sure your ~/.cshrc file has /usr/local/bin/ in your PATH variable. The PYTHONPATH variable must also be defined to include the location of YUP. You can find the required settings in ~curator/Shared/Resources/DOT-cshrc. You can copy it to your ~/.cshrc file, taking care to preserve your own settings.

The recommended text editor is TextWrangler. This program can be invoked from the command line as edit. If you have to use another editor make sure it can show up to 130 columns of text clearly on your display. Use a text editor that provides support for Python programming.

It is assumed that you work out of one directory: ~/Documents/work/.		 Resources

Yammp Under Python
The Harvey Laboratory

Python Home
Python Tutorial

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