[gmx-users] Concentration

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 26 22:12:15 CET 2008

Chih-Ying Lin wrote:
> Hi
> How to make a solution with specific concentration ?

Concentration of what?  For ions, use genion -conc; for other solute molecules, 
do some simple stoichiometry from General Chemistry based on the box volume.

> Command 1 =>
> editconf -d  0.75  -bt cubic
> 0.75=Distance between the solute and the box
> cubic = the type of the simulation box
> Command 2 =>
> genbox -cp solute.gro -cs spc.gro -box Y Y Y
> Y = the box vector in nm
> If I use cubic in my system, is Y defined as the length of the cubic in 
> the three directions?

Yes, that's what you've instructed genbox to do.

> Is the overall volume of the simulation box = Y * Y *Y  (nm*nm*nm) ?


> Is the center of cubic on the origin (0,0,0) of the coordinate?

No.  By convention, the system will be centered at (Y/2) in each direction.

If you're setting up your system using the above commands, it might be easier to 
just combine the box creation into one step with editconf (which will also print 
the coordinates of the system center): editconf -bt cubic -box Y -c


> Thank you
> Lin
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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