Difference between revisions of "2014 AMS-536 Spring"

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| '''Talk'''
 
| '''Talk'''
 
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| 2013.01.28 || '''First Day of Class and Organizational Meeting''' <br> Group Study || Mathlab account setup <br> Discuss research paper and presentations <br> handouts for unix / vim / csh tutorials
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| 2014.01.27 || '''First Day of Class and Organizational Meeting''' <br> Group Study || Mathlab account setup <br> Discuss research paper and presentations <br> handouts for unix / vim / csh tutorials
 
|-
 
|-
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| 2013.01.30 || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup  
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| 2014.01.29 || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup  
 
|-
 
|-
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| 2013.02.04 || Group Study || Continue unix / vim / csh tutorials <br> Logging into Seawulf  
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| 2014.02.04 || Group Study || Continue unix / vim / csh tutorials <br> Logging into Seawulf  
 
|-
 
|-
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| 2013.02.06 || Group Study || Finish unix / vim / csh tutorials <br> Csh scripting exercises <br> Transfering files to Seawulf
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| 2014.02.06 || Group Study || Finish unix / vim / csh tutorials <br> Csh scripting exercises <br> Transfering files to Seawulf
 
|-
 
|-
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| 2013.02.11 || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
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| 2014.02.11 || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
 
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| 2013.02.13 || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
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| 2014.02.13 || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
 
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| 2013.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf Allen, W.]
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| 2014.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf Allen, W.]
 
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| 2013.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2014.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2013.02.25 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2014.02.25 || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2013.02.27 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2014.02.27 || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2013.03.04 || Group Study || Tutorials: DOCK <br> wiki editing
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| 2014.03.04 || Group Study || Tutorials: DOCK <br> wiki editing
 
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| 2013.03.06 || Group Study || Tutorials: AMBER <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf Jiang L.]
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| 2014.03.06 || Group Study || Tutorials: AMBER <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf Jiang L.]
 
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| 2013.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion  
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| 2014.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
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| 2013.03.13 || Group Study || Tutorials: AMBER <br> individual project discussion  
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| 2014.03.13 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
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| 2013.03.18 || Spring Recess || Spring Recess
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| 2014.03.18 || Spring Recess || Spring Recess
 
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| 2013.03.20 || Spring Recess || Spring Recess
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| 2014.03.20 || Spring Recess || Spring Recess
 
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| 2013.03.25 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2014.03.25 || Group Study || Tutorials: AMBER <br> individual project discussion
 
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| 2013.03.27 || Group Study || Tutorials: AMBER <br> wiki editing
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| 2014.03.27 || Group Study || Tutorials: AMBER <br> wiki editing
 
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| 2013.04.01 || '''Deadline for project proposal discussion''' <br> Foda, Zack and Kasavajhala, Koushik || Project Proposal
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| 2014.04.01 || '''Deadline for project proposal discussion''' <br> Foda, Zack and Kasavajhala, Koushik || Project Proposal
 
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| 2013.04.03 || Ralph, Brian and Guo, Jiaye || Project Proposal
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| 2014.04.03 || Ralph, Brian and Guo, Jiaye || Project Proposal
 
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| 2013.04.08 || Shan, Jiahui and Krantsevich, Nick || Project Proposal
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| 2014.04.08 || Shan, Jiahui and Krantsevich, Nick || Project Proposal
 
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| 2013.04.10 || Xing, Weiliang and Stenzoski, Natalie || Project Proposal
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| 2014.04.10 || Xing, Weiliang and Stenzoski, Natalie || Project Proposal
 
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|-  
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| 2013.04.15 || Krantsevich, Artem and Chen, Yuan || Project Proposal
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| 2014.04.15 || Krantsevich, Artem and Chen, Yuan || Project Proposal
 
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| 2013.04.17 || '''Preliminary Report Due''' <br> Huang, He and Chen, Ye || Project Proposal  
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| 2014.04.17 || '''Preliminary Report Due''' <br> Huang, He and Chen, Ye || Project Proposal  
 
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| 2013.04.22 || Ralph, Brian and Kasavajhala, Koushik || Progress Report
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| 2014.04.22 || Ralph, Brian and Kasavajhala, Koushik || Progress Report
 
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| 2013.04.24 || Guo, Jiaye and Krantsevich, Nick || Progress Report
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| 2014.04.24 || Guo, Jiaye and Krantsevich, Nick || Progress Report
 
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| 2013.04.29 || Foda, Zach and Shan, Jiahui || Progress Report   
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| 2014.04.29 || Foda, Zach and Shan, Jiahui || Progress Report   
 
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| 2013.05.01 || Xing, Weiliang and Stenzoski, Natalie || Progress Report  
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| 2014.05.01 || Xing, Weiliang and Stenzoski, Natalie || Progress Report  
 
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|-
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| 2013.05.06 || Chen, Yuan and Krantsevich, Artem || Progress Report  
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| 2014.05.06 || Chen, Yuan and Krantsevich, Artem || Progress Report  
 
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|-
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| 2013.05.08 || '''Last Day of Class''' <br> Chen, Ye and Huang, He || Progress Report
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| 2014.05.08 || '''Last Day of Class''' <br> Chen, Ye and Huang, He || Progress Report
 
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| 2013.05.15 || '''Final written report due by 5PM today.  Late papers will not be accepted.  See above for sample reports and detailed guidelines.''' || '''Give hard copy to Yuchen Zhou (Math Tower room 3-129) and email electronic copy to Joe'''
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| 2014.05.15 || '''Final written report due by 5PM today.  Late papers will not be accepted.  See above for sample reports and detailed guidelines.''' || '''Give hard copy to Yuchen Zhou (Math Tower room 3-129) and email electronic copy to Joe'''
 
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|-
 
|}
 
|}

Revision as of 12:27, 23 January 2014


Instructor Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu]
Teaching Assistant Dr. William J. Allen [631-632-8519, william.allen@stonybrook.edu]
Course No. AMS-536 / CHE-536
Location/Time Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:30PM - 3:50PM
Office Hours Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
Acknowledgments The AMS-536 instructors would like to thank:

(1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses
(2) Yan Yu and the Seawulf team for cluster support
(3) Pat Tonra for Mathlab support


Project Information

Project Approval Sheet


Oral Presentation Guidlines: These meetings should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be 30 minutes long. The purpose of your talks is for you to clearly and concisely present your overall progress to date including appropriate background material and interpretation of your results. Talks should be arranged in the following order:

  • Introduction/Background (include biological relevance)
  • Specifics of Your System
  • Computational Details (theory)
  • Computational Details (system setup)
  • Results and Discussion (include a critical interpretation of your results)
  • Conclusions
  • Future
  • Acknowledgments


Final Report Guidelines and Example Final Papers


Tutorials, Software Links, and Other Relevant Class Information

Schedule

  • Each participant please update the Wiki as required with the title of your talk.
  • Please note that a doctors excuse will be required if you miss your scheduled oral presentation date because of illness.


Date Participant Talk
2014.01.27 First Day of Class and Organizational Meeting
Group Study 		Mathlab account setup
Discuss research paper and presentations
handouts for unix / vim / csh tutorials
2014.01.29 Group Study Confirm Mathlab accounts work
Go over unix / vim / csh tutorials
Seawulf account setup
2014.02.04 Group Study Continue unix / vim / csh tutorials
Logging into Seawulf
2014.02.06 Group Study Finish unix / vim / csh tutorials
Csh scripting exercises
Transfering files to Seawulf
2014.02.11 Group Study Visualization/analysis software
VMD, Chimera, and MOE
2014.02.13 Group Study Visualization/analysis software
VMD, Chimera, and MOE
2014.02.18 Group Study Tutorials: DOCK
individual project discussion Allen, W.
2014.02.20 Group Study Tutorials: DOCK
individual project discussion
2014.02.25 Group Study Tutorials: DOCK
individual project discussion
2014.02.27 Group Study Tutorials: DOCK
individual project discussion
2014.03.04 Group Study Tutorials: DOCK
wiki editing
2014.03.06 Group Study Tutorials: AMBER
individual project discussion Jiang L.
2014.03.11 Group Study Tutorials: AMBER
individual project discussion
2014.03.13 Group Study Tutorials: AMBER
individual project discussion
2014.03.18 Spring Recess Spring Recess
2014.03.20 Spring Recess Spring Recess
2014.03.25 Group Study Tutorials: AMBER
individual project discussion
2014.03.27 Group Study Tutorials: AMBER
wiki editing
2014.04.01 Deadline for project proposal discussion
Foda, Zack and Kasavajhala, Koushik 		Project Proposal
2014.04.03 Ralph, Brian and Guo, Jiaye Project Proposal
2014.04.08 Shan, Jiahui and Krantsevich, Nick Project Proposal
2014.04.10 Xing, Weiliang and Stenzoski, Natalie Project Proposal
2014.04.15 Krantsevich, Artem and Chen, Yuan Project Proposal
2014.04.17 Preliminary Report Due
Huang, He and Chen, Ye 		Project Proposal
2014.04.22 Ralph, Brian and Kasavajhala, Koushik Progress Report
2014.04.24 Guo, Jiaye and Krantsevich, Nick Progress Report
2014.04.29 Foda, Zach and Shan, Jiahui Progress Report
2014.05.01 Xing, Weiliang and Stenzoski, Natalie Progress Report
2014.05.06 Chen, Yuan and Krantsevich, Artem Progress Report
2014.05.08 Last Day of Class
Chen, Ye and Huang, He 		Progress Report
2014.05.15 Final written report due by 5PM today. Late papers will not be accepted. See above for sample reports and detailed guidelines. Give hard copy to Yuchen Zhou (Math Tower room 3-129) and email electronic copy to Joe
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