Hello all,
my colleague asked me if it is possible to do Steered MD using Amber
GPU implementation which means for the moment pmemd.cuda. I didn't
use this technique till now so I tried just simple test with sample input
code
(page 126 of Amber11 manual) below is the full input. This input was
accepted
and simulation was performed without any error but reqested "smd.txt" was
not created
so I am not sure if "ncsu_smd" part of my input was not simply ignored by
pmemd.cuda,
although I found the full input info written in *.out file.
Thanks in advance for relevant comments !
Best wishes,
Marek Maly
heat ras-raf
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000,dt=0.002,
ntc=2,ntf=2,iwrap=1,ioutfm=1,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0,
ig=-1,
temp0=310.0,
/
ncsu_smd
output_file = 'smd.txt'
output_freq = 50
variable
type = DISTANCE
i = (5, 9)
path = (X, 3.0) path_mode = LINES
harm = (10.0)
end variable
end ncsu_smd
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Received on Thu Jul 14 2011 - 10:30:02 PDT
