On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > 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.
I did another quick check, which regardless of my way of calculation. two cubic box, the same conc. I compared the ratio of Na+CL in two box is 24/60=0.4 while I compared the volumn ratio is 149.6/533.39=0.28. This way is easily for others to check too. read the ions from two topol.top and the dimension from two .gro. > > Hope it helps, Thanks, > > 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 > -- Best Regards, lina -- 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
