Re: PBC related query

From: Gianluca Interlandi (
Date: Wed Apr 25 2007 - 13:13:25 CDT

It can happen that the protein drifts towards one side of the box. This is
usually not a problem. The part of the protein outside the box is not in a
vacuum because the water box is replicated at infinity in all three space
directions. In fact, you will see a "hole" in the water at the other side
of the box.

The protein will be wrapped around once the geometric (or mass?) center
will have passed the box limit.


On Wed, 25 Apr 2007, wrote:

> Hi all,
> I am doing an NVE run with PBConditions where i observe my protein
> drifting towards one side of box and some portion is already out. I
> am using "wrapall ON" option. Can someone suggest how can i see the
> part of protein going outsidebox which will reenter from other end?
> Is it bad if it drifts to one side? Any suggestion will do great.
> regards
> Harish
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823

Dr. Gianluca Interlandi
                    +1 (206) 685 4435
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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