Dear all,
I have been using the Gaussian accelerated MD in AMBER18 for the first
time. I have a few doubts regarding the same. So my input has been the
following. Initially I had done a 100ps NVT production and used that rst
file to begin the GaMD production.
&cntrl
imin = 0,
irest = 0, ntx = 1,
nstlim = 19000000, dt = 0.002,
ntc = 2, ntf = 2, tol = 0.000001,
iwrap = 1, ntb = 1, cut = 8.0,
ntt = 3, temp0 = 300.0, tempi = 300.0,
ntpr = 50, ntwx = 50, ntwr = 500,
ntxo = 1, ioutfm = 1, ig = -1, ntwprt = 22,
igamd = 3, iE = 1, irest_gamd = 0,
ntcmd = 1000000, nteb = 3000000, ntave = 50000,
sigma0P = 6.0, sigma0D = 6.0,
&end
1. How is the total time for this is calculated. For the classical MD, it
is nstlim * dt
2. Do I need to restart the GaMD simulation as per the normal protocol? I
have not seen an elaborate tutorial for that GaMD part like the others for
AMBER18.
3. How should one proceed with the free energy calculation of the GaMD
part? Could someone suggest an elaboorate tutorial covering the scripts and
analysis part of this for a beginner just like we have for all other
methods in AMBER.
Apologies if the questions are trivial.
Regards,
Sruthi Sudhakar
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Received on Wed Dec 09 2020 - 03:30:02 PST
