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

Justin Lemkul jalemkul at vt.edu
Mon Oct 8 20:45:40 CEST 2012

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?


> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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