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
&cntrl
irest=1, ntx=5,
ibelly=0, imin=0,
nstlim=100,
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,
&end
&ewald
use_pme=0, vdwmeth=0, eedmeth=4, ischrgd=1,
&end
dhfr: input filename:mdin (found in run filename benchmark)
-----
equilbrate apo-dhfr
&cntrl
ntb=1,
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,
&end
4096wat: input filename: gbin (found in run filename benchmark)
--------
short md, nve ensemble
&cntrl
ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=100, ntt=0,
ntpr=25, ntwr=10000,
dt=0.001,
&end
Nathalie
--
------------------------------------------------------------------------
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
