Use Linux-x86_64-multicore and the following script to set CPU affinity:
namd2 +setcpuaffinity `numactl --show | awk '/^physcpubind/ {printf \
"+p%d +pemap %d",(NF-1),$2; for(i=3;i<=NF;++i){printf ",%d",$i}}'` ...
For runs on large numbers of cores (you will need to experiment) use the following to enable the Charm++ communication thread:
namd2 +setcpuaffinity `numactl --show | awk '/^physcpubind/ {printf \
"+p%d +pemap %d",(NF-2),$2; for(i=3;i<NF;++i){printf ",%d",$i}; \
print " +commthread +commap",$NF}'`