AMBER Archive (2004)

Subject: Re: AMBER: solute leaving PBC box

From: myang_at_vitamin.uni.cc
Date: Thu Oct 07 2004 - 17:00:09 CDT

As far as i know. It's ok.
You may use ptraj to wrap the solute back into the box.

On Thu, Oct 07, 2004 at 04:24:47PM -0500, opitz_at_che.udel.edu wrote:
> Dear Amber Community,
>
> I am running MD in a periodic box, with the following input:
> &cntrl
> imin=0, irest=1, ntx=5,
> iwrap=1,
> ntb=2, ntp=1, pres0=1, taup=1.0
> ntf=1,
> igb=0,
> ntr=0, cut=12,
> ntt=1, tempi=300, tmp0=300, tautp=1
> nstlim=2600000, dt=0.01, t=400,
> ntpr=1000, ntwx=1000, ntwr=1000
> &end
> At the end of this I took a look at my simulation, and my solute (the
> molecule of interest), has migrated through the box to one of its
> corners. Parts of the molecule are sticking out of the box, and aren't
> imaged back into the box.
> Does this affect the molecule behavior? If so how could i prevent it from
> leaving the box?
> Please help.
>
> Best Regards,
>
> Armin
>
>
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