README

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                                  Molecular3D
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Authors:
  Abhinav Bhatele
  Edgar Solomonik


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			   INSTRUCTIONS FOR COMPILING
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1. Run the copy_namd.sh script (specify a correct path for namd inside the
script) in the src_namd folder
NOTE: NAMD source from 2010-04-01 will definitely work

2. Do make in the compile folder


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                             INSTRUCTIONS FOR RUNNING
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To run specify three parameters:

1. A NAMD configuration file (such as apoa1.namd)
2. The branching factor (default set to 2), and
3. A load balancing strategy

i.e. ./charmrun +p8 ./mol3d apoa1.namd 8 +balancer DummyLB

run from the same folder as namd parameter files (need a .js format file)
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