RE: [AMBER] simulation under pressure

From: Yang Li <chlorin316.hotmail.com>
Date: Mon, 29 Mar 2010 19:53:01 +0000

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
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