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Building Amber PMEMD Version 9 From Source Code on Blue Gene/L


Important Notes

First Steps Regardless of Whether PMEMD 9 is Built With or Without MASSV

  1. Order and obtain Amber 9.
  2. Place the tar.gz file in /home/johndoe/pmemd9.
  3. Study the AMBER page describing the config files for PMEMD 9 for the IBM Blue Gene/L.

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Building PMEMD 9 Without the MASSV Libraries

  1. Copy the Amber 9 tar.gz file from /home/johndoe/pmemd9 to /home/johndoe/pmemd9-nomassv, gunzip it and extract the resulting tar file.
  2. Download the config file from the
    AMBER page describing the config files for PMEMD 9 for the IBM Blue Gene/L
    and,naming it config.h, place it in
    /home/johndoe/pmemd9-nomassv/amber9/src/pmemd.
  3. Set environment variables.
  4. cd /home/johndoe/pmemd9-nomassv/amber9/src/pmemd
  5. make install
  6. The pmemd executable will be created in /home/johndoe/pmemd9-nomassv/amber9/exe .

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Building PMEMD 9 With the MASSV Libraries

  1. Copy the Amber 9 tar.gz file from /home/johndoe/pmemd9 to /home/johndoe/pmemd9-massv, gunzip it and extract the resulting tar file.
  2. Download the config file from the
    AMBER page describing the config files for PMEMD 9 for the IBM Blue Gene/L
    and,naming it config.h, place it in
    /home/johndoe/pmemd9-massv/amber9/src/pmemd.
  3. Modify config.h .
  4. Set environment variables.
  5. cd /home/johndoe/pmemd9-massv/amber9/src/pmemd
  6. make install
  7. The pmemd executable will be created in /home/johndoe/pmemd9-massv/amber9/exe .

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