i have ran a particular MD of protein in water for 100ps (50,000 steps) in a variety of combinations
1. on a single processor( non-mpi) intel core2duo 2.2Ghz 2 GB ram time taken : 1hr 30 min 2. 2 processors on a single machine (MPI) similar specs time taken : 35 min 3 .2 processors on different machines (mpi) similar specs time taken : 1hr 5 min 4 .5 processors on 5 different machines (mpi) similar specs time taken: 38 min 5.10 processors on 5 different machines(mpi) similar specs time taken: 45 min OS for 1- open discovery ( fedora 9) for 2-5 Rocks cluster 5.1 network connectivity Gigabit on cat6 Are the above specified time intervals normal or i am making big big mistakes. comments are invited. kala bharath
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