[MDseriesmar2012-news] Preparations for Upcoming OpenMM Workshop

[Joy P. Ku]

Dear Workshop Participant:
 
We're excited about your attendance at the OpenMM workshop in a couple of
weeks.  We have created this mailing list to correspond with you and also
for you to correspond with others that are attending the workshop.
 
Below is the agenda for the workshop.  The workshop will be held in Room
123 in the Munger Graduate Residences.  For directions, parking
instructions, and other helpful logistical information, visit
http://simbios.stanford.edu/EventsOfInterest/logisticsMDWorkshopFeb2012.ht
m. 
 
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
by end-of-day next Tuesday (March 6th).  Instructions below.
 
As you will see from the agenda, there will be time for you to work on
your own projects and receive individual assistance on using OpenMM.
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 soon!
 
Best,
Joy
 
 

INSTALLATION INSTRUCTIONS

 

1.        Install VMD, the molecular visualization tool we will be using
in the workshop. 
- Go to  <http://www.ks.uiuc.edu/Research/vmd>
http://www.ks.uiuc.edu/Research/vmd 
- Click on "Download VMD" and select the installation for your platform.

 

2.       You will need OpenMM 4.0.  Go to  <https://simtk.org/home/openmm>
https://simtk.org/home/openmm. 
- Click on "Downloads" 
- Download the Documentation file OpenMMApplicationGuide.pdf.  Follow the
instructions in Chapter 2 to set up OpenMM and if applicable, install the
GPU software. 
- Verify your installation by running the testInstallation.py program

 

3.       Email us:  Send the results of running testInstallation.py to
simbiosfeedback at stanford.edu.  If you encounter problems along the way,
you can email us at that same address.

 

 

AGENDA (TENTATIVE)

 


Monday, March 12, 2012

 	

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

Introduction to Running Simulations with OpenMM

- Peter Eastman 

 

 	

10:45am - 11:00am

BREAK

 	

11:00am - 12:00pm

 

Exercises:  Running Simulations with OpenMM

- You, guided by Diwakar Shukla 

 	

12:00pm - 1:00pm

LUNCH (on your own) 

 	

1:00pm - 1:30pm

Introduction to the OpenMM API

- Peter Eastman

 

 	

1:30pm - 2:15pm

Exercise:  Creating Custom Forces

- You, guided by Peter Eastman

 

 	

2:15pm - 3:00pm

Exercise:  Using AMOEBA Polarizable Force Fields

- You, guided by Lee-Ping Wang

 

 	

3:00pm - 3:15pm

BREAK

 	

3:15pm - 3:30pm

 

Discussion:  Breakout Groups and Topics

- Everyone, led by Joy Ku

 

 	

3:30pm- 5:00pm

Work on your own research questions with support from the OpenMM team and
others in your breakout group

- You, guided by Peter Eastman, Diwakar Shukla, and Lee-Ping Wang

 

 	

5:00pm 

Reception

 	




Tuesday, March 13, 2012


9:30am - 10:00am

Creating New Force Fields in OpenMM

- Peter Eastman 

 


10:00am - 10:30am

Validation of OpenMM 

- Peter Eastman

 


10:30am - 10:45am

BREAK

 


10:45am - 11:30am

Alchemical Free Energy Calculations and OpenMM

- John Chodera 

 


11:30am - 12:30pm

LUNCH (on your own)

 


12:30pm - 4:00pm

Work on your own research questions with support from the OpenMM team and
others in your breakout group

- You, guided by Peter Eastman, Diwakar Shukla, and Lee-Ping Wang

 


4:00pm- 4:30pm

Wrap-up:  Sharing of Useful Tips and Tricks

 

 

				

 

 

_______________________________________________

 

Joy P. Ku, PhD

Director, 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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