Hi Geoffrey,
I believe that AMBD calculations are only available in sander. Please see here: http://archive.ambermd.org/201203/0022.html
Cheers,
Parker
-----Original Message-----
From: Geoffrey Gray [mailto:gmgray2.mail.usf.edu]
Sent: Tuesday, February 25, 2014 4:21 PM
To: AMBER Mailing List
Subject: [AMBER] Adaptive Biasing calculations
I am currently attempting to run adaptive biasing calculations on several torsions using Amber12. I tried running some tests using the examples provided in the doc files, but while the dynamics ran, no information regarding the biasing was printed. I used the following script:
-------------------------------
Langevin dynamics
&cntrl
imin=0, irest=1, ntx=5,
ntt=3, gamma_ln=2.0,
ntc=2, ntf=2, dt = 0.002, nscm=0,
nstlim=7500000, ig=-1, isgld=0,
ntwe=0, ntwx=1000, ntpr=5000, ntwr = 1000000,
ntb = 0, cut = 999.0, rgbmax=15.0,
igb = 8, saltcon=0.150,ioutfm=1,
tempi=300., temp0=300.,
/
ncsu_abmd
mode = FLOODING
monitor_file = 'abmd.dat'
monitor_freq = 500
timescale = 1.0
variable
type = DISTANCE
i = (2824,2826)
min = 0. max = 10.
resolution = 0.5
end variable
end ncsu_abmd
/
&wt type='END'
/
------------------------------
I am currently using pmemd.cuda, but have also tried with pmemd.MPI and gotten the same results. Thanks in advance for your help.
Geoffrey Gray
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Received on Tue Feb 25 2014 - 14:30:02 PST
