Hi;
I'm running a GBSA simulation of a 4000 atom protein (Amber 7 on a
linux platform). The simulation
is taking a bit more than I expected (approximately 8 hours for 13000
steps). I was wondering how frequently are the GB integrals/surface area
calculations performed? I didn't see a way to adjust it in the GBSA
section of the manual. Below is my input to sander. Thanks
-Sergio
Equilibration for implicit solvent
&cntrl
imin = 0,
nmropt = 1,
ntpr = 1000, ntwx = 1000,
ntwr = 1000,
ntf = 2, ntb = 0,
cut = 12,
igb =1, gbsa = 1,
nstlim = 100000,
t = 0.0, dt = 0.001,
temp0 = 300.0, tempi = 100.0,
ntt = 1, dtemp = 0.0,
ntp = 0,
taup = 1.0,
ntc = 2, tol = 0.00001,
&end
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Received on Wed Feb 11 2004 - 23:53:00 PST
