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 :) Cheers, Tsjerk > > -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 > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
