[gmx-users] gromacs preformance versus amber
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 21 21:54:57 CET 2007
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:
> 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
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