[gmx-users] how to calculate the conc in the genion

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 11 20:11:52 CEST 2011

Hey Justin,

> I'm wondering if you can elaborate a bit on this.  I can understand your
> point in the case of interfacial systems, membranes, or other biphasic
> systems, but for a protein in water, why does the volume occupied by the
> protein matter?  All components - protein, water, ions - are all part of the
> same phase and contribute to the total volume.  Experimentally, one simply
> adds the desired amount (either dry or from concentrated stock) and dilutes
> to the necessary final volume.  There is no distinction made for volume
> occupied by a protein, substrate, or buffer component.  Is this distinction
> really necessary in the simple case of a protein in water?  I'd be curious
> to hear your thoughts.

The protein will be solved in some solution that has a specified
amount of salt, as well as other stuff. That solution thus has a
specific water to salt ratio. Let's assume there is no specific
interaction between protein and salt, then in the vicinity of the
protein there will be the same ratio of water to salt. If you cut out
a small portion, containing the protein, and warp opposite ends so as
to make it periodic, there should still be that same water to salt
ratio. The volume of the protein is not suddenly also occupied by some
ions. Vice versa, mimicking such a solution in silico is best done by
adding ions up to the water to ion ratio that corresponds to the
concentration of the medium. Of course, if you consider the whole
system, the protein will have an insignificant effect on the volume
and the distinction between molarity and molality won't matter much.
But if you cut out a piece of about the scale of the protein, then it
will make a difference. Note that interactions between the protein and
the salt will mess things up, but you can't really say a priori in
which way.

I'd be happy to hear further arguments of the contrary though :)



> -Justin
>> Whether the number of water molecules matters for the calculation of
>> the ion concentration depends on the unit you use for concentration.
>> Probably  molality is a better option than molarity. For that you do
>> take the number of water molecules. Frankly, that's what I usually do.
>> Doing so will give a desired concentration of ions in the solvent,
>> regardless of volume occupied by other (big) solutes or by nothing.
>> There is just one problem that stays nonetheless; in how far does the
>> bulk concentration you use as target correspond to the local
>> concentration you might need to use? Solutes, membranes and voids may
>> alter the local concentration significantly.
>> By the way, Lina, it would have helped if you had given the equations,
>> numbers and outcomes that lead you to believe there is something
>> wrong.
>> Hope it helps,
>> Tsjerk
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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