Dear Amber users,
I am using the following input parameters for doing the production run of
classical MD simulation with Amber.
NVT md with random seed and netCDF output format
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 2000, ntwx = 2000, ioutfm = 1,
ntc = 2, ntf = 2,
ntt =3, gamma_ln=2.0, ig=-1,
nstlim = 3000000, dt =0.002,iwrap=1,
tempi = 300.0, temp0 = 300.0, tautp =2.0,
ntb = 1, ntp = 0, taup = 2.0, pres0 =1.0,
&end
Following a standard protocol, I did minimization and extensive (10-20 ns)
equilibration of the protein-water system before entering to production
run. But, I am a little confused about the use random seed generator in
production. As per Amber manual, ig=-1 will generate different random seed
and thereby different staring velocity for each simulation window ( say one
use a 5 ns window for doing a 100 ns long simulation). Such a change in
velocity can bring changes in the phase space for every run ( ie, the run
may not be a continuation of previous window). If that the case, what is
the point of doing extensive equilibration here?
Many thanks
Anu
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Received on Tue Mar 15 2016 - 05:30:04 PDT
