[gmx-users] Making composite box in gromacs

[Justin Lemkul]

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 <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
>>
>> ========================================
>>

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

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

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