Re: protein diffuses to boundary..

From: George Madalin Giambasu (
Date: Wed Mar 07 2007 - 18:15:08 CST

are you constraining the protein at the center of the sphere? if not, that's
what is going to happen if your system is charged: your system inside the
sphere doesnot "feel" any electrostatic response from the outside, and the
protein is going to diffuse to the boundary.

the simple solution is to constrain the protein to the center of the sphere.
the more complicated one (involving coding :( ), is to implement smth like
GSBP , VEP, or smth similar.

I hope this helps,


On 3/7/07, <> wrote:
> Hi All,
> I have this problem where my protein is diffusing to wall of my
> spherical boundary. Diffusing in the sense that after a few nanoseconds,all
> of it drifts towards the solvent spherical boundary. I guess one solution to
> avoid this is to make big sphere or conduct simulation in a periodic box.
> But i want to know some solution presently for spherical boundaries so that
> it does not drift and interact with my spherical boundary or say walls.
> Thanks in advance for any help.
> Harish
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823

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