AMBER Archive (2009)

Subject: [AMBER] atoms fly out of the box in NVT calculations

From: iccy liu (
Date: Thu Feb 12 2009 - 15:48:24 CST


Thanks a lot for your kind help in advance.

I met a very strange situation. I set up a NVT calculation with periodic bounary condition using the input script below. However when I checked the trajectory and restart file, I found out the box size is the same as in my inpcrd file, however there are several molecules (more than 20) are out of the box. Some of them are 20A away from the bounary. I couldn't figure out why. My understanding is that if a molecule move out of the box, the peridic boundrary conditions will place it back in the other side of the box. Did anyone has similar problem before? Or just my input file has problems and the simulation wasn't go as the way I thought? Any input will be highly appreciated.

input scirpt

  imin=0, irest=0, ntx=1,
  nstlim=5000, dt=0.0005,
  ntc=2, ntf=2,
  tempi=0.0, temp0=50.0,
  ntpr=100, ntwx=500, ntwx=1000,
  ntb=1, igb=0,



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