[gmx-users] Re: salt solution
oliver at biop.ox.ac.uk
Fri Nov 26 21:53:11 CET 2004
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.
> 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
Oliver Beckstein * oliver at biop.ox.ac.uk
More information about the gromacs.org_gmx-users