[gmx-users] Re: Simulation of a protein confined in a box

[Matthew Hoopes]

As you may have seen in the GROMACS 4.0 manual, "Walls can only be used with
pbc=xy" so its more of a floor/ceiling. You still may want a solution beyond
the feature mentioned in chapter 7. Particle based realizations for walls
may
be a bit more work but very doable. See the following paper.

Chenyue Xing and Roland Faller J. Phys. Chem. B, 112 (23), 7086-7094, 2008.

-Matt



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Message: 3
Date: Sat, 11 Oct 2008 10:41:39 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Simulation of a protein confined in a box
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <48F0BB23.7030108 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Lee Soin wrote:
> This seems to me a very complicated realization. Why doesn't
> GROMACS provide an easy way for wall simulation?
>

How about reading manual section 7.3.20 "Walls" in the Gromacs-4.0 manual?
I 
think that would be what you're after.

-Justin


> 2008/10/11 Omer Markovitch <omermar at gmail.com <mailto:omermar at gmail.com>>
> 
>     Oh, I didn't read carefully.
>     My suggestion would be, perhaps, to physically put atoms on the
>     sides of the box (possibly, fill each side completely), and to place
>     on them very high repulsion.
>     You might want to freeze them up, and exclude their self
>     interactions from the energy calculation.
> 
>     Good guess Suman. Omer.
> 
>      
>     Koby Levy research group,
>     Weizmann Institute of Science.
>     http://www.weizmann.ac.il/sb/faculty_pages/Levy/
> 
> 
>     On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty
>     <suman at sscu.iisc.ernet.in <mailto:suman at sscu.iisc.ernet.in>> wrote:
> 
>         Possibly what he is interested in is a system WITHOUT PBC? I
>         don't think
>         with PBC the system is really "confined", since there is no true
>         wall to
>         reflect the colliding molecules. Thus to study the effect of real
>         confinement, it is necessary to remove PBC and impose reflective
>         boundary conditions. I am only guessing! :)
> 
> 
>         --Suman.
> 
> 
> 
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> 
> 
> -- 
> Sun Li
> Department of Physics
> Nanjing University, China
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================