[gmx-users] Binary mixture

[Justin Lemkul]

On 9/15/17 11:14 AM, spss4 at iacs.res.in wrote:
>   ----- Message from Justin Lemkul <jalemkul at vt.edu> ---------
>      Date: Fri, 15 Sep 2017 11:12:37 -0400
>      From: Justin Lemkul <jalemkul at vt.edu>
> Reply-To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Binary mixture
>        To: gmx-users at gromacs.org
> 
>> On 9/15/17 10:59 AM, spss4 at iacs.res.in wrote:
>>> Hi all
>>> I want to prepare a  cubic box of 6M urea. How many molecules of urea
> and
>>> how many water molecules should be added to the simulation box? How to
>>> calculate these numbers? Please help me to solve this.
>>
>> Everything depends on the size of the box, which is somewhat arbitrary.
>> If you have a volume, you can easily calculate the number of molecules
>> required to reach the desired molarity.
>>
>> -Justin
>>
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
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> 
> If my box size is 343 nm^3 then how I can calculate the number of urea and
> water?
> 

Convert to liters, calculate the number of molecules.  This is simple unit 
transformation from general chemistry (and not really a topic for this list, 
since you don't really have a GROMACS problem).

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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