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,
/
It's been a while since I used AMBER, but this looks like straight
cut-off electrostatics at 8 angstrom (vomit!). Thus you're comparing
apples with oranges, since GROMACS is using PME. You will need a
thorough understanding of the options in both AMBER and GROMACS to come
up with a sensible simulation that is fairly comparable.
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.
The rate-determining step in all MD simulations is the calculation of
the non-bonded interactions. Once you choose comparable algorithms here,
the assembly-optimized routines for GROMACS will likely stomp all over
AMBER. The "implementation of the force field" is way down the list of
importance.
You will also likely want to compare single-processor jobs.
Mark
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