[Mdseriesmay2011-news] Simbios MD Workshop Series - Preparing for the Workshop

[Joy P. Ku]

Dear workshop participant:
 
We're excited about your attendance at the MD workshops next week.  The
agenda for the day is given below.  The workshop will be held in the Doll
Conference Room in the Gunn-SIEPR building at 366 Galvez Street.  For
directions, parking instructions, and other helpful logistical
information, visit 
http://simbios.stanford.edu/EventsOfInterest/logisticsMDWorkshopMay11.htm
.
 
Please help us ensure the workshops run smoothly.  We will be covering a
lot of material, so we ask that you install the needed software packages
before the workshop.
 
Installation instructions are provided here:
http://simbios.stanford.edu/EventsOfInterest/MDMay11Instructions.htm
 
Please email us at simbiosfeedback at stanford.edu
<https://simtk.org/mailman/listinfo/mdseriesmarch10-day1>  to let us know
if you were successful in the installation process. 
 
There will be time for you to work on your own projects and receive
individual assistance on using OpenMM and
MSMBuilder.  Please remember to bring the necessary files for you to work
on your own.
 
If you are unable to attend for any reason, please let me know as soon as
possible so that we can accept people from our wait list. 
 
Thank you.  I look forward to meeting you next week!
 
Best,
Joy
 

 

 


Monday, May 23, 2011


9:30am - 9:40am

Welcome and introduction of instructors and workshop attendees

- Vijay Pande


9:40am - 10:00am

Introduction of OpenMM & Roadmap

- What is it, what is it not, our goals, what's new, etc:  Vijay Pande


10:00am - 10:45am

OpenMM API

- Peter Eastman 

 


10:45am - 11:00am

BREAK


11:00am - 11:30am

 

Introduction to OpenMM's Python API

- Peter Eastman 

 


11:30am - 12:00pm

Exercise:  "Hello Argon" - writing your first program with the OpenMM API

- You, guided by Michael Sherman

 


12:00pm - 1:30pm

LUNCH (on your own) 


1:30pm - 2:30pm

Exercise:  Beyond moving atoms - delving deeper into the OpenMM API

- You, guided by Michael Sherman

 


2:30pm - 3:30pm

Exercise:  Using OpenMM's CustomForce classes

- You, guided by Peter Eastman

 


3:30pm - 3:45pm

BREAK


3:45pm - 4:15pm

 

Introduction to integrating OpenMM into a molecular dynamics package

- Peter Eastman 

 


4:15pm- 4:45pm

Introduction to AMOEBA

- Mark Friedrichs

 


4:45pm - 5:00pm

Wrap-up

 


5:00pm 

Reception

 

 


Tuesday, May 24, 2011


9:30am - 9:40am

Welcome and introduction of instructors and workshop attendees

- Vijay Pande


9:40am - 10:40am

Introduction to trajectory analysis  

-Vijay Pande


10:40am - 11:00am

BREAK 


11:00am - 12:30pm

Introduction to MSMBuilder  (hands-on)

- You, with guidance from Greg Bowman

 


12:30pm - 1:30pm

LUNCH (on your own)

 


1:30pm - 4:30pm

Work on your own research questions with support from the OpenMM and
MSMBuilder developers 

 


4:30pm- 5:00pm

Wrap-up

 

 

 

 

_______________________________________________

 

Joy P. Ku, PhD

Director of Dissemination, Simbios

 <http://simbios.stanford.edu> http://simbios.stanford.edu

 

Director of Communications & Training,

National Center for Simulation in Rehabilitation Research

 <http://opensim.stanford.edu> http://opensim.stanford.edu

 

(W)  650.736.8434, (F)  650.723.7461

Email:   <mailto:joyku at stanford.edu> joyku at stanford.edu

 

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