[gmx-users] comparison of reaction field and PME

[Yuguang Mu]

Dear Users,

First of all thank you all for the answers for the parallel problem.
Now we have scceed in running parallel jobs using LAM version of MPI.

Here I found another thing:

I check two nearlly identical simulations of peptides in DMSO 
each is 20 ps long.

The other difference is the treatment of electro-static interactions
one  using reaction field (cut -off  )
rlist               =  1.2
rcoulomb            =  1.2
rvdw                =  1.2
coulombtype         =  Reaction-Field


Aother one is PME.
rlist               =  1.2
rcoulomb            =  1.2
rvdw                =  1.2
coulombtype         =  PME 
fourierspacing      =  0.1
pme_order           =  4
optimize_fft        =  yes

The simulation results are all reasonable, no problem.

But the CPU time used by PME are nearlly 4 times longer that CUT-OFF.

here is the output for CUT-OFF :
               NODE (s)   Real (s)      (%)
       Time:    331.000    331.000    100.0
                       5:31
               (Mnbf/s)   (MFlops) (ps/NODE hour) (NODE hour/ns)
Performance:     10.283    477.522    217.523      4.597


and here is PME
               NODE (s)   Real (s)      (%)
       Time:   1294.000   1294.000    100.0
                       21:34
               (Mnbf/s)   (MFlops) (ps/NODE hour) (NODE hour/ns)
Performance:      2.631    451.218     55.641     17.972


Do you think it is normal?
Or further optimize the FFTW codes is necassary?

Yuguang