This case study presents the results of porting a production scientific code, called NAMD, to the SRC-6 high-performance reconfigurable computing platform based on Field Programmable Gate Array (FPGA) technology. NAMD is a molecular dynamics code designed to run on large supercomputing systems and used extensively by the computational biophysics community. NAMD's computational kernel is highly optimized to run on conventional von Neumann processors; this presents numerous challenges to its reimplementation on FPGA architecture. This paper presents an overview of the SRC-6 architecture and the NAMD application and then discusses the challenges, solutions, and results of the porting effort. The rationale in choosing the development path taken and the general framework for porting an existing scientific code, such as NAMD, to the SRC-6 platform are presented and discussed in detail. The results and methods presented in this paper are applicable to the large class of problems in scientific computing.