chemistry benchmark query

[G. Ravishanker <ravishan |-at-| swan.wesleyan.edu>]

 Hi
 We purchased three IBM RISC/6000 Powerstations last fall. Our primary
 research is in the area of molecular simulations, using Molecular Dynamics
 and Monte Carlo simulations. We also have another group doing
 electrostatic models for proteins. The time hog in all these are the
 molecular simulations. The molecules we study are DNA and protein and our
 systems range in size from 600 atoms (for vacuum simulations) to about
 7000 (for aqueous solutions). We also run the MD simulations for about
 200-300 picosecond range.
 Our experience so far has been extremely good. We use a program called
 WESDYN, which was derived from another MD program called GROMOS. Our
 typical benchmarks show that the speed we get is between 1/8 to 1/10th of
 the CRAY Y-MP time. Given that we have these boxes give 24 hrs of
 dedicated processor time, compared to getting 2-3 hrs of CRAY time a day,
 we are sort of breaking even in terms of throughput. We are able to run 10
 picosecond of dynamics on a system of 6000 atoms in 24 hours (clock time).
 The machine is very easy to install. The service engineers are extremely
 helpful, though they are not fully knowledgeable. They try all sorts of
 channels to get the problems solved quickly. The OS is pretty stable and
 the on-line documentation called info-explorer takes a while to get used
 to, but is great. X-Windows works great for the most part. (It is only X11
 Rev. 3 compliant) Silicon Graphics GL programs work great for the most
 part. The scheme of opening and resizing windows does not work exactly the
 way it does on Silicon Graphics machines, but most other operations work
 just fine. We have had Polygen Quanta, a molecular modeling program up and
 running on the IBM RISC for the past two months and are pretty happy with
 it.
 Overall, we are very pleased with the speed of the machine and its overall
 stability. We have had instances where the student runs the machine
 continuously for a week to 10 days. The only complaint we have is the lack
 of manuals. One needs to purchase it for a price. IBM wants everyone to
 use the info-explorer. This is fine when the machine is up and running.
 When one has only one machine and the machine goes down, it creates a big
 problem. The price is very attractive for the MFLOPS/MIPS ratio of the
 Powerstation 530. There are reasonable public domain software already
 available, such as TeX and emacs.
 Hope this is useful and if you need further info, please feel free to let
 me know.
 Ravi