Re: protein diffuses to boundary..

From: hl332_at_drexel.edu
Date: Wed Mar 07 2007 - 18:59:01 CST

Thanks for your reply but i did not understand your reasoning. My system (overall) is not charged firstly because i make it neutral before run. Also, why my it will not feel electrostatics is not clear. It will do great if you cab be more explicit. Further, how to make center of sphere coincide with spherical boundary and stay there all the time.

thanks a lot in advance for your interest. PLease do reply.

Harish

-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: George Madalin Giambasu <giambasu_at_gmail.com>
Date: Wednesday, March 7, 2007 7:15 pm
Subject: Re: namd-l: protein diffuses to boundary..

> 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,
>
> george
>
> On 3/7/07, hl332_at_drexel.edu <hl332_at_drexel.edu> 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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