Thanks for your help! I appreciate it
Geoffrey
On Tue, Feb 25, 2014 at 5:14 PM, de Waal, Parker <Parker.DeWaal.vai.org>wrote:
> 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 - 17:00:03 PST
