Hi all,
I am currently running QM/MM ncsu_abmd for free energy calculation. It is just a simple proton transfer from water to O atom (of GTP). I have three questions:
1. As explained in the ABMD theory article, there should be two control parameters for governing the ABMD, The flooding time scale Tf and the kernel width 4∆ξ, but I do not have idea how to control this kernel width in ABMD input?
2. I want ABMD to study a distance rang of H(from water) - O (from GTP) from 1.8A to 1.0 A, but actually the ABMD seems is not studing the full sapce, it stayes at around 1.8~1.5A.
My input file is at the end of my email
3. Is there any other method in Amber who can do the similiar work as ABMD, for enhanced free energy simulation?
thanks!
aixiao
&qmmm
qmmask=':*',
qmcharge=0,
qm_theory='AM1D',
qmshake=0,
writepdb=1,
/
ncsu_abmd
mode=FLOODING
monitor_file='abmd.txt'
monitor_freq=100
umbrella_file='umbrella.nc'
timescale=90.0 !
variable
type = DISTANCE ! distance H-O
i = (8,9)
min=1.00 max=1.80
resolution=0.25
end variable
end ncsu_abmd
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Received on Fri Nov 28 2014 - 09:30:02 PST
