[gmx-users] Re: salt solution

Oliver Beckstein oliver at biop.ox.ac.uk
Fri Nov 26 21:53:11 CET 2004

Hi Burri,

when I want to simulate an electrolyte then I first create a simulation
box with solvent (and a protein). (If you simulate a bulk electrolyte you
only need 'genbox -cs -box X Y Z'.)

- count the number of water molecules, NW. (eg 'grep OW file.gro | wc')
- calculate the number of ions that you need for a given concentration
  (basic physical chemistry) from the total volume occupied by the solvent
  (if you have a box of water then you obviously know the volume V already
  but if you have solvated a protein with irregular shape then you can use
  the number of water molecules to estimate the volume)

  c+ : conc of cations
  cW : conc of water 
       rW : density of water, 0.997 g/cm^3
       MW : molec weight of water, 18.02 g/mol  

       cW = rW/MW = 55.3 mol/l	

  vW : molar volume of water

       vW = 1/cW

  V:   total volume of solvent

       V = nW * vW    (nW: amount of water in mol)

  Hence the numer of cations (in mol) is

       n+ = c+ * V = nW * c+/cW

  or just as simple numbers

       N+ = NW * c+/cW

  Calculate N- in the same way.

- use 'genion -np N+ -nn N- ...' to insert the appropriate amount of ions.


  Found NW = 877 water molecules. Want a target concentration of 1M NaCl,
  hence c+ = c- = 1M:

  c+ = 877 * 1/55.3 = 15.85 =~ 16

  So use 'genion -np 16 -nn 16 ...'.

Hope that helps. If in doubt consider the man pages/help functions of
genbox and genion.

Note: In some inhomogeneous systems (eg with protein/membrane or system
with cavities, especially when hydrophobic) your real final concentration
in the bulk regions of your simulation box can be *higher* than what you
aimed for because an exclusion layer can develop which only contains water
but no ions (similar for hydrophobic cavities/channels), and the ions are
expelled into the bulk regions.

Btw, I forwarded this to gmx-l so that other people might benefit from
the reply as well, and it gets archived for future reference.

Best wishes,

> Dear Oliver,
> I found your mailid from gmx-user group, I want ask you some help regarding
> salt solution gro file. Please can you possible to tell how to make different
> concentration salt solution gromacs structure files. If you have any
> concentration gro file, please send for me.
> Thank you very much for your time and consideration
> Looking for positive reply.
> Till Then
> Burri

Oliver Beckstein * oliver at biop.ox.ac.uk

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