[gmx-users] Re: salt solution

eric jakobsson jake at ncsa.uiuc.edu
Sat Nov 27 00:08:58 CET 2004

Good description.  One other point---if the protein is not neutral, you may 
want to think carefully about whether to make the whole system neutral by 
giving an excess of either negative or positive ions.  In our simulations 
we do that, so the whole system is neutral.  Our reasoning is that a 
charged protein will, in nature, attract an excess of oppositely charged 
ions to its vicinity that neutralize the charge, so that if you have more 
than a Debye length of water (about 10 angstroms at physiological 
concentrations) around the protein you have net electroneutrality.

At 02:53 PM 11/26/2004, you wrote:
>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
>  http://sansom.biop.ox.ac.uk/oliver/
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Eric Jakobsson, Ph.D.
Professor, Molecular and Integrative Physiology, Biophysics and 
Computational Biology, Beckman Institute, Bioengineering, Biochemistry, and 
Senior Research Scientist, National Center for Supercomputing Applications
4021 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Avenue
Urbana, IL 61801
ph 217-244-2896
fax 217-244-2909
e-mail jake at ncsa.uiuc.edu

(Since May 2003 I have been on leave from the University of Illinois to 
serve as the Chair of the NIH Biomedical Information Science and Technology 
Consortium and the NIGMS Center for Bioinformatics and Computational 
Biology, in Bethesda, Maryland.  However I commute to Urbana almost every 
week to maintain my research lab here. 

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