[AMBER] flying out

From: William Flak <williamflak.yahoo.com>
Date: Mon, 23 Aug 2010 21:02:38 -0700 (PDT)

Dear AMBER
It may be a naive question, sorry for that.
During my simulation, I equilibrated my system for 100 ps and started my production phase, during production phase I found my molecule (a molecule in a box of water) flied out the box of water (around 500 A away from the water box) and the system was crashed. I checked its position during the equilibration, it was fine.
Here is my mdin file for the production phase:


 &cntrl
  imin= 0,
  irest=1,
  NTX=5,
  ntb=2,
  ntp=1,
  PRES0=1.0,
  TAUP=2.0,
  NTPR=1000,
  NTWX=1000,
  ntave=1000,
  ntr=0,
  Tempi=300.0,
  Temp0=300.0,
  NTT=3,
  gamma_ln=1.0,
  NTC=2,
  NTF=2,
  cut=12.0,
  nstlim=250000,
  dt=0.002,
  icfe=1,
  clambda=0.5
 /
  
Any kind of help would be appreciated.
Thanks in advance
W. Flak




      


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Received on Mon Aug 23 2010 - 21:30:03 PDT
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