[gmx-users] Re:Re: gromacs preformance versus amber (David van der Spoel)

[servaas michielssens]

> Message: 1
> Date: Wed, 21 Nov 2007 21:54:57 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] gromacs preformance versus amber
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47449B21.7030803 at xray.bmc.uu.se>
> 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.