Suggestions while building a GPU-machine (CUDA) for NAMD use!

From: Aditya Ranganathan (
Date: Mon May 27 2013 - 03:14:33 CDT

Hello All,

We are pondering over investing on a GPU based machine for running NAMD
simulations (all-atom). Currently, we are stuck with a dilemma over the
choice of card for CUDA computing. We already have a GTX 680 which gives us
about 3ns/day for a 100000 atom system using a single GPU card and 8 cpu

Now, we are planning to build a GPU machine with 4 GPU cards (either Tesla
C-2075C, 6GB GDDR5 or the NVIDIA GTX 680). The base system would consists
of a 6-core Intel Xeon E5 2620 processor, 64GB DDR3 RAM and a 2TB Hard

Has anyone in the community used the Tesla series of cards with NAMD and
compared its benchmarks (scalability etc) with a entry level card like GTX
680. The cost of the Tesla is almost 3 times that of the GTX680. Does its
performance justify its price?

Any suggestions from the community would be greatly appreciated.


Srivastav Ranganathan
Research Scholar
IIT Bombay,
Mumbai, India

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