Grid Computing for Biomolecular Studies

1
Grid Computing for Biomolecular Studies

• Celia Croy
• Monash University
• Melbourne, Australia
• August 14, 2006

2
This Weeks Progress

• Performed GAMESS/APBS calculations in subsequent
  NIMROD experiments using the previous
  experiments optimized coordinates as input for
  the next higher basis set calculation
• Altered coordinate extraction scripts to create
  GAMESS input files with more variable keywords
  for versatility of application
• Analyzed data by comparing optimized coordinates
  from each GAMESS calculation to determine if
  higher basis set calculations are necessary
• Organized output files and data to prepare for
  database deposit

3
Also

• Researched possibilities for improvement of the
  NIMROD/GAMESS/APBS pipeline by addition of an
  infinite dilution activity coefficient (IDA)
  calculation
• Studied up on basic computational chemistry
  concepts, methods, basis sets and approximations
• Contacted Kim Baldridge, Celine Amoreira and
  Laura Berstis in Switzerland via VTC to discuss
  final project goals

4
Final Project Goals

• Register for more resources to use with NIMROD if
  current resources are down
• Perform final basis set calculations and
  determine if higher basis set calculations are
  needed diffuse functions, electron correlation,
  etc.
• Extract data from GAMESS/APBS calculations for
  database deposit
• Continue to discuss future plans and project
  goals with mentors
• Prepare PowerPoint for seminar at Monash
  University and write paper

5
DOCKLANDS