[gmx-users] gromacs preformance versus amber

[servaas michielssens]

I am considering to use gromacs for MD-simulation for speed reasons, so
I tried to compare a amber simulation to a gromacs simulation. I ran a
20ps simulation with amber. I converted my topology and coordinate file
from amber to gromacs using and tried the same run in gromacs.
amb2gmx.pl(http://chemistry.csulb.edu/ffamber/). This is my amber input:


&cntrl
  imin=0,nstlim=10000,nmropt=0
  irest=1,ntx=5,
  iwrap=1,
  nscm=1000,
  dt=0.002,
  ntb=2,ntp=1,
  ntt=1,tautp=1.0,temp0=300.0,
  ntc=2,ntf=2,
  cut=8.0,
  ntwx=250,ntpr=250,
/

This is my gromacs input:

title           = FWS
cpp             = /usr/bin/cpp
constraints     = all-bonds
integrator      = md
dt              = 0.002 ; ps !
nsteps          = 10000 ; total 20 ps.
nstcomm         = 1000
nstxout         = 250 ; collect data every 1 ps
nstlog          = 0
nstenergy       = 250
nstvout         = 0
nstfout         = 0
nstlist         = 10
ns_type         = grid
rlist           = 1.0
coulombtype     = PME
rcoulomb        = 1.0
vdwtype         = cutoff
rvdw            = 1.4
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on
Tcoupl          = berendsen
tau_t           = 1.0 1.0
tcgrps          = protein non-protein
ref_t           = 300 300
; Pressure coupling is on
Pcoupl          = parrinellorahman
tau_p           = 0.5
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocites is on at 300 K.
gen_vel         = no
gen_temp        = 300.0
gen_seed        = 937475
                                                                                                                                          

I ran it on 4 AMD Opteron(tm) Processor 250. It turned out that amber
could simulate 1.5ns/day and gromacs only 1ns/day. This was a surprise
to me, I expected that gromacs would be faster.  Could it be that using
gromacs with the amberFF is not faster than just using amber? I am new
to gromacs and perhaps I didn't compare them correct.

kind regards,

servaas michielssens