NAMD Wiki: NamdOnCrayXE6
See also NamdOnCrayXT5.
To get NAMD 2.8 to run on a Cray XT, add -DNOHOSTNAME -DNO_GETPWUID to the CXX definition in CRAY-XT-g++.arch and use the modified Tcl library from http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-crayxe.tar.gz or http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-crayxe-threaded.tar.gz (for SMP builds).
The following has been reported to work as of Feb 8, 2011 using the development versions of Charm++ and NAMD:
Switch to gcc with module swap PrgEnv-pgi PrgEnv-gnu
Remove -lrca from charm/src/arch/mpi-crayxt/conv-mach.sh
Compile charm as ./build charm++ mpi-crayxt -j8
Compile namd as ./config CRAY-XT-g++