The YASARA Benchmarks
Since the first YASARA website went online in 1999, we have been providing benchmarks to allow an objective comparison with other programs. Our goal is however not to start 'benchmark wars' with other groups, as we are all trying to solve the same problems. So instead of comparing other programs with YASARA directly, we offer symbolic rewards of 100$ for the first one who can beat YASARA in one of the following benchmarks. (You do not have to use your own program, just anything you find).
The following restrictions apply:
Benchmark 1: 100$
for a faster molecular dynamics algorithm
The image on the right shows a classic molecular
dynamics benchmark: dihydrofolate reductase (PDB entry 1AOE) and 6875
summing up to 23788 atoms. You can download the PDB
file here. Here we measure the time required for one full
simulation step of a standard MD protocol using the AMBER03 force field
and TIP3P water:
Here are the execution times on various
CPU types (single-core only, see next benchmark for multi-core
performance). In our hands, especially the SSE4.1 code path is about 60%
faster than the closest competitor (measured in 32-bit Linux with
standard GCC compiler).
Today, even entry level CPUs contain more than one core. While the single-core performance in the previous benchmark is a good measure for the degree of optimization and algorithmic tuning, in practice the multi-core performance is more important. The system simulated here is the same as in the previous benchmark, but multiple CPU cores are used now. The numbers below are for static load balancing, i.e. if you run the same simulation a second time, you will get the same trajectory. This is very important for several, but not all applications of MD. If your program can beat YASARA only with dynamic load balancing (and thus non-reproducible trajectories, covering a smaller range of applications), the reward is cut to 50$.
Here are the execution times on a growing number of CPU cores:
On the left, you can see the unit cell of PDB entry 2A0B:
the phosphotransfer domain of anaerobic sensor kinase ARCB, solved at
1.57 Å resolution. The cell contains four chains, and thanks to the
high resolution, provides a very accurate view of protein structure.
Running a molecular dynamics simulation of such a crystal moves the
protein away from where it should be, due to inaccuracies in the force
field. The smaller the damage, the more accurate the force field.
During a 1 nanosecond simulation with YASARA's YAMBER2 force field, the
maximum Calpha RMSD from the true structure is 0.70 Å. 100$ are yours
if you manage to obtain a lower RMSD with any MD program / force field
you like, under the condition that you did not optimize the force field
specifically for 2A0B or its homologues.
The screenshots on the left show PDB entry
1N8R, the 50S ribosomal subunit with 98569 atoms, in space-filling
mode. In the upper image, all atoms are on screen, YASARA delivers
frames per second without shadows (many programs are a factor 35
slower), or 5.5 frames per second with shadows calculated in real-time
(as shown). On the lower
image, we flew right through the ribosome to the backside, most atoms
are now off-screen, resulting in 106 frames per second without shadows
(as shown). To win the 100$,
your program must be faster in both cases (either with or without
shadows), while reaching at least the
same visual quality (e.g. spheres must be equally round), and it must
run on the same or a slower system.
molecular modeling during a real-time molecular dynamics simulation
allows you to pull individual atom and entire molecules around with the
mouse or 3D input devices. The image on the right shows the simulation
of dihydrofolate reductase (see benchmarks 1 and 2 above for details),
including all water molecules. Using four CPU cores on the system
described below, YASARA reaches 12 frames per second, i.e. 12 molecular
dynamics steps and 12 screen updates including real-time shadows. To
win the 100$,
your program must be faster on the same or a slower system and reach at
least the same visual quality.