AMBER Archive (2009)

Subject: Re: [AMBER] part of the protein escaped from the water box

From: Jason Swails (
Date: Thu Oct 15 2009 - 06:43:00 CDT

This should not affect your results. Because you're using periodic boundary
conditions, your simulation is feeling the effect of the waters in the
adjacent boxes, but the trajectory files show only a single box. Such are
the issues with visualizing such a dynamic periodic system with only one
box. If you have a non-covalently bound ligand docked somewhere in your
protein, you may even see that fly across the box if it gets too close to
the edge of the current box you're visualizing. Rest assured that this,
too, is simply an artifact of this 'box confusion' of sorts.

Best of luck!

On Thu, Oct 15, 2009 at 7:33 AM, qiaoyan <> wrote:

> Dear everyone:
> I simulate a protein including 104 residues, the protein was surrounded
> by a periodic box of water molecules described by the TIP3P potential
> extended to a distance of 10.0A from any solute atom. After 6ns of
> constant-pressure simulation, part of the protein escaped from the waterbox,
> I don't know whether this phenomenon affect the result, please help me,thank
> you!
> The script I use is as follows:
> &cntrl
> imin=0,
> ntx=5, irest=1,
> ntpr=100, ntwx=1000,ntwr=5000,
> dt=0.002,nstlim=1000000, nscm=1000,
> cut=9.,dielc=1.0,iwrap=1.0,
> ntc=2, ntf=2,
> ntb=2,
> ntp=1,pres0=1.0,taup=3.0,
> ntt=1, tautp=3.0,temp0=300.0,
> ioutfm=1
> /
> Have a nice day!
> qiaoyan
> 2009-10-15
> qiaoyan
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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