From joyku at stanford.edu Fri May 20 01:00:50 2011 From: joyku at stanford.edu (Joy P. Ku) Date: Fri May 20 01:00:52 2011 Subject: [Mdseriesmay2011-news] Simbios MD Workshop Series - Preparing for the Workshop Message-ID: <001b01cc16c3$e1e951e0$a5bbf5a0$@edu> 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 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 Director of Communications & Training, National Center for Simulation in Rehabilitation Research http://opensim.stanford.edu (W) 650.736.8434, (F) 650.723.7461 Email: joyku@stanford.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: https://simtk.org/pipermail/mdseriesmay2011-news/attachments/20110520/b7a30461/attachment-0001.html From joyku at stanford.edu Fri May 20 01:21:31 2011 From: joyku at stanford.edu (Joy P. Ku) Date: Fri May 20 01:21:33 2011 Subject: [Mdseriesmay2011-news] Simbios MD Workshop Series - Preparing for the Workshop Message-ID: <002a01cc16c6$aa16fa30$fe44ee90$@edu> 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 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 Director of Communications & Training, National Center for Simulation in Rehabilitation Research http://opensim.stanford.edu (W) 650.736.8434, (F) 650.723.7461 Email: joyku@stanford.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: https://simtk.org/pipermail/mdseriesmay2011-news/attachments/20110520/086e73b0/attachment-0001.html