[gmx-users] gromacs preformance versus amber

[David van der Spoel]

servaas michielssens wrote:
> 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.
> 
Did you run gromacs in parallel at all?
Did you get four md.log files, one for each processor?


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se