[gmx-users] Re: gmx-users Digest, Vol 107, Issue 133

[Abhinav Agrawal]

Actually my doubt was how to make a simulation box from two structure files
i.e. how do i keep the clay and poymer boxes close to each other to run
energy minimization

 Message: 4
> Date: Sun, 31 Mar 2013 07:38:38 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Making composite box in gromacs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <5158203E.3020609 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/31/13 6:38 AM, Abhinav Agrawal wrote:
> > I have polymer and clay structures and I need to study their surface
> > interaction. How do I keep a clay box on top of polymer.
> >
>
> The concepts of "top" and "bottom" are irrelevant in a periodic system.
>  You can
> position anything within the unit cell wherever you like with editconf
> -center.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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