Under the folder $SPEC/benchspec/CPU2017/544.nab_r/Docs/ there will be a script called makeprm.sh.
It is
used to produce inputs for the NAB benchmark. To use it, you must have the
AmberTools toolset installed. This was the only script used to produce inputs
for the benchmark.
All inputs were found in the RCSB protein database
Note: That script fails for many of the proteins. The reason is unknown but it seems that proteins with modified residues tend to fail. The inputs included in this workload were created by selecting proteins that can be processed successfully.
Each workload also needs a "control" file, with each line containing the following 3 parameters:
Where directory is the name of a directory in the input folder containing the output from makeprm.sh, seed is a seed for the number generator, and steps is the number of simulation steps to perform.