On 3/31/13 2:22 PM, Abhinav Agrawal wrote:
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
Consider the following:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
The logic holds for any interfacial or inhomogeneous system. Place whatever
species you want, wherever you want them in the box, with editconf -center,
-translate, -rotate, etc as necessary.
-Justin
Message: 4
Date: Sun, 31 Mar 2013 07:38:38 -0400
From: Justin Lemkul <[email protected]>
Subject: Re: [gmx-users] Making composite box in gromacs
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
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
========================================
--
========================================
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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