Dear users,
I have some basic questions regarding running SGLD simulation in amber14.
This is the input i am using for running SGLD for RNA folding:-
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2,
ntr = 0,
pres0 = 1,
ntp = 1,
taup = 2.0,
cut = 10.0,
ntc = 2,
ntf = 2,
tempi = 310.0,
temp0 = 310.0,
ntt = 3,
ig = -1,
ioutfm = 1,
iwrap = 1,
gamma_ln = 1.0,
nstlim = 500000, dt = 0.002, tol = 0.00001,
ntpr = 1000, ntwx = 1000, ntwr = 50000, ntwprt=864,
isgld=1, tsgavg=0.2, tempsg=315
/
The total no of atoms in my system are 359214 (including waters), but i am
printing only 1-864 atoms in the trajec file..However, a run of 1ns takes
approx 72-75 hrs to finish. (40 xeon cores , E52680)
1.) In explicit solvent conditions, does the guiding force is limited to
only solute or is applied to solvent molecules also? Is this why 1ns run is
taking this much time?
2.) Can i use something like isgsta=1 and isgend=864 to specify the range
on which guiding force should be applied?
Thanks
Asmita
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Received on Thu Jul 16 2015 - 04:30:04 PDT
