Message: 1
Date: Wed, 21 Nov 2007 21:54:57 +0100
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] gromacs preformance versus amber
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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?
Thanks for you answer,
Yes this worked fine, I have a log file for every processor, their must be
some other problem. I also tried to run it on 8 or 16 processors, here the
run failed. Amber runs worked fine, so I don't think their are problems with
the processors
kind regards,
servaas michielssens.
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