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

[Justin A. Lemkul]

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.
> 
> 
> 
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> -- 
> Sun Li
> Department of Physics
> Nanjing University, China
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

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