Hi, Dr. Case,
Thank you for you recommendations. I checked and my prmtop was
periodic and solvated. I tried to run a 10 step simulation, here is my
input file.
DNA 12-ATmer simulation under 100atm
&cntrl
imin = 0, irest = 1,
igb = 0, ntx = 5,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
ntp = 1, taup = 2.0, pres0 = 100,
ntb = 2, ntc = 2, ntf =2,
nstlim = 10, dt = 0.01
ntwx = 1, ntpr =1
cut = 12.0
/
However, the simulation has run for the entire weekend again and did
not finish on the 3G processor.
Please let me know what I can do.
With regards,
Yang
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Received on Mon Mar 29 2010 - 13:00:04 PDT
