1. –resethway: At the start of each simulation, GROMACS tunes the domain decomposition and balances the load between available CPUs and GPUs. This slows down the first few hundred iterations. Because real simulations run for a very long time this does not have any impact on achieved performance. To minimize the runtime needed to obtain stable results while benchmarking the option –resethway should be specified. -resethway resets all performance counters when half of the iterations are executed and thus allows to measure realistic performance without many time steps. Note that if the reset occurrs while the PME load balancer is still active in the beginning of the run, the following error may occur "PME tuning was still active when attempting to reset mdrun counters at step xxxxxxx". To avoid this you can increase the running time steps by increasing the -maxh used or adding -nsteps parameter to increase the number of timesteps of the simulation.
2. -maxh: Controls the maximum time the simulation should run. mdrun executes enough time steps to run at least for the specified time in hours. This should be set to a high enough value to obtain stable performance results. A reasonable value would typically be 5 Minutes = 0.08333. Either this option or the "nsteps" option described below can be used to limit the running time of the simulation.
3. –noconfout: This disables the output of confout.gro which might take a considerable amount of time e. G. on parrallel file systems. As this is done very infrequent in real simulations, this should be disabled during benchmarking.
4. –v: Print out more information to the command line and the produced log file md.log. The contained information is very helpful to tune the performance of GROMACS.
5. –nb: This tells GROMACS to use either "gpu" or "cpu" for certain calculations
6. –nsteps: number of timesteps to run. Overrides the default value in the mdp file. This option can also be used to control the overall time that a simulation will run instead of using the maxh.
The Performance is reported at the end of the produced log file (md.log) as well as on the console output in ns/day (higher is better).
Visit GROMACS documentation page to get additional details about the command line parameters.