Dear AMBER community,
I have performed GaMD equilibration on a protein-ligand system using the
dual boost scheme (boost potential and boost dihedral) utilizing the
following input file:
&cntrl
imin = 0, irest = 0, ntx = 1,
nstlim = 5000000, 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 = 200, nteb = 200, ntave = 100,
sigma0P = 6.0, sigma0D = 6.0,
&end
When I opened the gamd.log file, I realized after a few frames, the
"Total-Force-Weight" and "Boost-Energy-Potential" are 1.000000000000
and 0.000000000000 respectively. Is this a normal behavior? As the boost
energy potential is zero, I wonder if the GaMD simulation (with boost
potential) is really running or not?
I have attached the gamd.log file with some initial and final frames.
I shall be very happy to receive any feedback on this.
Thank you in advance...
Best
Jac
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- application/octet-stream attachment: gamd1.log
Received on Sun Feb 21 2021 - 01:00:02 PST
