On Fri, Aug 12, 2011 at 8:08 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 12/08/2011 2:22 AM, lina wrote: >> >> 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. >>> >> Yes. I do agree with you. >> >> Here I have a field problem, I will be very glad if I can be told >> which part of calculation is wrong. >> >> a cubic box: Volumn = 101.57 *105.03 * 87.82 A = 9.369E-25 m^3 = >> 93.69E-23 L >> total ions: 121 >> >> so the concentration based on the box volume is: >> >> 121/AvagadroConstant/Volumn = >> 121/6.022E23/93.69E-23=121/6.022/9.369=0.214 mol/L? >> >> But before when I used -conc, the number I chose maybe 0.1 or 0.15 >> mol/L, but not 0.2mol/L. > > That's the concentration of total ions, but the concentration of each ionic > species is about half that.
Thanks, I should not have used total number of ions. > > Mark > >> >> Here if consider the water, certainly the water volumn will be greatly >> smaller than the box volumn, so the concentration will reach very >> high? >> >> I might be wrong in some way, hope someone can point out. >> >> Thanks, >> >>> 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 >>> >> >> > > -- > 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
