Hi, >> I'd be amazed if the error was in the code and not in your calculation. The >> number of water molecules doesn't matter for the calculation of the ion >> concentration, of course. Pay attention to your box shape. And do consider >> the number of ions has to be an integer, so for a given volume you cannot >> get arbitrarily close to a given concentration.
The error is, to my humble opinion, in the reasoning. Concentration is a macroscopic property, and when dealing with a minute volume, the concentration of something in it is ill defined. Especially when there's something else in that volume, taking up a significant amount of space, like a membrane, protein or void, it becomes troublesome. I would argue that the worst you can do in that case is take the volume of the box and calculate the number of things to add from there to reach a given concentration. 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 -- 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
