[gmx-users] Re: gmx-users Digest, Vol 102, Issue 52

[Justin Lemkul]

On 10/8/12 7:48 AM, Ali Alizadeh wrote:
> Dear usres
>
> Thank you for your replies
>
> 1- Is it possible define a ion as a propane molecule and then
> I do adding propane molecules instead of methane molecules in my system?
>

Unlikely.

> 2- Other wise, I select 300 molecules  of methane and remove them from my
> system(randomly and by hand, for example 500 molecules of methane and
> adding 100 molecules of propane,)
> [Dr. Vitaly Chaban comment]
>
>          Is it possible and common method?
>

I think the best approach is contained in the link I already posted.  Place 
within whatever number of molecules of the minor species (propane) you want in 
the box, and then "solvate" with the major species (methane).

-Justin

-- 
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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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