There are two data sets in UEABS for Gromacs. 1. ion_channel that use PME for electrostatics, for Tier-1 systems 2. lignocellulose-rf that use Reaction field for electrostatics, for Tier-0 systems. Reference : http://pubs.acs.org/doi/abs/10.1021/bm400442n The input data file for each benchmark is the corresponding .tpr file produced using tools from a complete gromacs installation and a series of ascii data files (atom coords/velocities, forcefield, run control). If it happens to run the tier-0 case on BG/Q use lignucellulose-rf.BGQ.tpr instead lignocellulose-rf.tpr. It is the same as lignocellulose-rf.tpr created on a BG/Q system. The general way to run gromacs benchmarks is : WRAPPER WRAPPER_OPTIONS PATH_TO_GMX mdrun -s CASENAME.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logile CASENAME is one of ion_channel or lignocellulose-rf maxh : Terminate after 0.99 times this time (hours) i.e. gracefully terminate after ~30 min resethwat : Reset Timer counters at half steps. This means that the reported walltime and performance referes to the last half steps of sumulation. noconfout : Do not save output coordinates/velocities at the end. nsteps : Run this number of steps, no matter what is requested in the input file logfile : The output filename. If extension .log is ommited it is automatically appended. Obviously, it should be different for different runs. WRAPPER and WRAPPER_OPTIONS depend on system, batch system etc. Few common pairs are : CRAY : aprun -n TASKS -N NODES -d THREADSPERTASK Curie : ccc_mrun with no options - obtained from batch system Juqueen : runjob --np TASKS --ranks-per-node TASKSPERNOD --exp-env OMP_NUM_THREADS Slurm : srun with no options, obtained from slurm if the variables below are set. #SBATCH --nodes=NODES #SBATCH --ntasks-per-node=TASKSPERNODE #SBATCH --cpus-per-task=THREADSPERTASK The best performance is usually obtained using pure MPI i.e. THREADSPERTASK=1. You can check other hybrid MPI/OMP combinations. The execution time is reported at the end of logfile : grep Time: logfile | awk -F ' ' '{print $3}' NOTE : This is the wall time for the last half number of steps. For sufficiently large nsteps, this is half of the total wall time.