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The Cray MTA-2 (Multithreaded Architecture) is an unusual parallel supercomputer that promises ease of use and high performance. We describe our experience on the MTA-2with a molecular dynamics code, SIMU-MD, that we are using to simulate the translocation of DNA through a nanopore in a silicon based ultrafast sequencer.Our sequencer is constructed using standard VLSI technology and consists of a nanopore surrounded by Field Effect Transistors (FETs). We propose to use the FETs to sense variations in charge as a DNA molecule translocates through the pore and thus differentiate between the four building block nucleotides of DNA.We were able to port SIMU-MD, a serial C code, to the MTA with only a modest effort and with good performance. Our porting process needed neither a parallelism support platform nor attention to the intimate details of parallel programming and interprocessor communication, as would have been the case with more conventional supercomputers.