AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Feb 12 2009 - 20:22:57 CST

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_at_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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