[Fwd: Re: SGI_MP and sander 6] input files

From: Nathalie Godbout <godbout_at_sgihud.hudson.sgi.com>
Date: Wed 04 Oct 2000 08:09:53 -0700

Hi everyone,

  To avoid any confusion as to what input files I used for the benchmark
runs I sent yesterday, here are the details, including the input files:

Those benchmarks were run with the Amber6 source code. I used the input
files found in the individual ``test'' directory as they were (all have
nstlim=100). For prowat, the input was mdin.6 (and not Run.plast), for
dhfr, the input (mdin) is included in the file called benchmark (and not
Run.dhfr) and for 4096wat, the input (gbin) is included in the file
called benchmark (and not Run.pure_wat).

prowat: input file name: mdin.6
# sander: Eqlbrtn of waters const T , SHAKE, cut=12.0
    irest=1, ntx=5,
    ibelly=0, imin=0,
    t=0.0, dt=0.0010, vlimit=20.0,
    ntt=1, temp0=300.0, dtemp=0.0, tautp=0.2,
    ntb=1, ntp=0,
    ntc=2, tol=0.0005, ntf=2,
    cut=12.0, scnb=2.0, scee=2.0,
    ntpr=50, ntwr=1000,
    use_pme=0, vdwmeth=0, eedmeth=4, ischrgd=1,

dhfr: input filename:mdin (found in run filename benchmark)
equilbrate apo-dhfr
    scnb=2.0, scee=1.2, ntpr=25,
    ntc = 2, ntf=2,
    nstlim = 100, temp0=300.0,
    ntt=0, dt=0.001, tau
tp=1.0, ntx=7, irest=1, vlimit=10.0,
    ntp=0, taup = 2.0,
    plevel=2, ntwr=1000,

4096wat: input filename: gbin (found in run filename benchmark)
short md, nve ensemble
   ntx=5, irest=1,
   ntc=2, ntf=2, tol=0.0000001,
   nstlim=100, ntt=0,
   ntpr=25, ntwr=10000,


Nathalie Godbout, Ph.D.       SGI 
godbout_at_hudson.sgi.com        Chemistry and Biology Applications Group
(781)839-2147                 One Cabot Road, Suite 250
(978)562-7450 fax             Hudson, MA     
vnet:483-2147                 01749, USA
Received on Wed Oct 04 2000 - 08:09:53 PDT
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