[gmx-users] Comparing Gromacs versions

[Djurre de Jong-Bruinink]

Dear all,

We recently did some comparisons of gmx 4.5.5, 4.6.1+group and 4.6.1+verlet cutoff scheme. The system was a protein (amber99) in water (tip3p) in a triclinic box (23k atoms total). We're using pme with a realspace cutoff=0.9nm, gridspacing=0.12nm, npme=-1, which based on g_tune_pme gives (close to) best performance. Below some performance measure (ns/day) from 100,000 step runs:

CPUs     G455        G461+group               G461+verlet
24            34.9          43.1                       35.3
36            47.6          57.8                       49.7
48            50.8          65.9                       60.4
60            59.9          81.8                       71.1
72            57.7          78.7                       78.2

The scaling to more CPUs in 4.6.1 is much better (thank you developers for putting up all the hard work!), however I would have expected more improvements from the verlet scheme. Note that both 455 and 461 have been compiled with MPI only (no OMP, GPU), and 461 was compiled with gcc (4.7.2). I did change the nstlist from 5 to 10 for the verlet scheme only.


Are these results expected given the setup? Is there anything I'm doing wrong?

Thanks in advance,
Djurre de Jong