Yammp 2 Workshop: August 16 to 18, 2005

Yammp 2 Workshop (3)

Georgia Institute of Technology

Cherry Emerson 312/4

Tuesday August 16 to Thursday August 18, 2005

YUP or Yammp 2 is a molecular mechanics program designed for multiscale models. The distinctive feature of this program is the use of Python as a programming and scripting language. This workshop is designed to teach participants to implement new models in Yammp 2. This means programming in Python.

Before the Workshop

Participants must complete Module 0 before the Workshop. This means learning to program in Python. Pay particular attention to Classes (and object oriented programming in general). The tutorial is most likely insufficient. You should look at other tutorials (start from the Python.org site) or even work from a textbook. The most important thing is to have some real Python programming experience and to get used to object-oriented programming before you come to the Workshop.

Modules

0
Preparations
1
Model Construction and Simulations
2
Programming with YUP Part 1
3
Programming with YUP Part 2
4
Force Field Assembly

Schedule

Monday August 15, 2005

This is an optional day when we will work through the exercises in Chapter 4 of Module 0. You do not need to have YUP installed for this module. If you are having difficulty with these exercises then we can spend the day working with you. Please let us know if you are coming.

08:00am Setup: introduction to MacOSX, change password, setup workspace, kinemage
Programming Exercises: develop a browser for PDB files
08:30am Module 0 Chapter 4: Preparations - complete Chapter 4 Exercises A to D
12:00pm Lunch break
01:00pm Module 0 Chapter 4: Preparations - complete the remaining exercises in Chapter 4
06:00pm End

Tuesday August 16, 2005

08:00am Setup: introduction to MacOSX, change password, setup workspace, kinemage
Model Building and Simulations: illustrated by the rrDNAv1 reduced representation DNA model
08:30am The rrDNAv1 model; the objects involved in simulations
09:30am Complete Module 1: Model Construction and Simulations
12:00pm Lunch break
Programming Part I: access to the internal data structures of Yammp 2
01:00pm The objects that make up a Yammp 2 model
01:30pm Module 2: Programming with YUP Part 1
06:00pm End

Wednesday August 17, 2005

Programming Part 2: writing scripts and programs; force field assembly
08:00am Introduction to scripting and programming
08:30am Work on Module 3: Programming with YUP Part 2
12:00pm Lunch break
Force Field Assembly
01:00pm Introduction to force field assembly
Implementing a new model type:
01:30pm Discussion: lessons learned from the development of the rrDNAv1 and rrRNAv1 models

Study Module 4: Force Field Assembly at any time; there are a few practical tips that might be helpful to know before you start to program.
06:00pm End

 

Thursday August 18, 2005

This day is spent in informal discussion of your model type and we will consider ways of implementing it. Please let us know if you are staying for this discussion.