AMBER Archive (2006)

Subject: AMBER: Failure of iwrap in PMEMD

From: Myunggi Yi (
Date: Thu Jul 20 2006 - 09:01:07 CDT

Dear Amber users,

I found the failure of image control (iwrap) in PMEMD (amber8).
As time goes by, more and more water molecules came out of
the primary box in my simulation.

I have never seen this before using SANDER (iwrap).
The following is my input, and I haven't found any error,
warning, and weired thing in the output file.

npt eq
  nstlim = 1000000, dt=.002,
  irest=1, ntpr=500, ntwx=500, ntx=5,
  temp0=310.0, ntt=1,
  tautp=2.0, taup=2.0, cut=9.0,
  ntb=2, ntp=2, iwrap=1,
  ntc=2, ntf=2,

I know this won't effect the simulation, and
I can handle this using ptraj in the post analysis.

Is there anything wrong in my input?

Best wishes,

MYUNGGI YI ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306

Office: (850) 645-1334 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to