Thanks Dr. Walker and Carlos Simmerling for his earlier reply as well. Yes, reimage it in ptraj works pretty well.
Iccy
> Date: Thu, 12 Feb 2009 21:22:57 -0500
> Subject: Re: [AMBER] atoms fly out of the box in NVT calculations
> From: ross.rosswalker.co.uk
> To: amber.ambermd.org
>
> Hi Iccy,
>
> Please see section 5.2.3 of Tutorial B1 :
> http://ambermd.org/tutorials/basic/tutorial1/section5.htm This will explain
> what you are seeing. It is an imaging issue and nothing to worry about. You
> can either reimage as explained in the tutorial or set iwrap=1 in the $cntrl
> namelist.
>
> All the best
> Ross
>
> 2009/2/12 iccy liu <hbliu92.hotmail.com>
>
> >
> > Hi,
> >
> > 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
> > ---------------------------
> >
> > &cntrl
> > imin=0, irest=0, ntx=1,
> > nstlim=5000, dt=0.0005,
> > ntc=2, ntf=2,
> > ntt=1,
> > tempi=0.0, temp0=50.0,
> > ntpr=100, ntwx=500, ntwx=1000,
> > ntb=1, igb=0,
> > cut=12.
> > /
> > ----------------------
> >
> >
> > Sincerely,
> >
> > Iccy
> >
> > _________________________________________________________________
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> >
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Received on Mon Feb 16 2009 - 01:12:17 PST
