Hmmm, Now imagine your simulation system as a say 1000 nm3 portion of a liter. For that liter you work out the number of ions and you properly translate that into an amount of ions you expect in the 1000 nm3. But then your protein (floating along in the same liter in some small concentration) crosses your small volume and you have a snapshot of a simulation system. Will the concentration of ions be what you would get if you would work out the volume (which is what genion -conc does)? Or should you consider how many moles of water you have in the system and work out the stochiometry? And what about the effect of the protein on the local salt concentration? A lot of homework for that poor first-year chemistry student.
Tsjerk On Fri, Jun 6, 2008 at 1:53 PM, Miguel Machuqueiro <[EMAIL PROTECTED]> wrote: > At 12:24 AM 6/6/2008, you wrote: >> >> jayant james wrote: >>> >>> Hi all !! >>> I want to add 150mM KCl into a cubic box that contains a protein in an >>> aqueous environment. How am I to calculate as to how? many Ions of K and Cl, >>> I need to add to bring to the above said salt conc? >> >> This sounds like a homework exercise for a first-year chemistry student! >> Work out the volume, then use the concentration to get a number of ions. >> >> Mark > > Hi Mark > > Just out of curiosity... how do you "work out the volume"? > > Miguel > > > ======================================== > Miguel Machuqueiro > ITQB-Instituto de Tecnologia Química e Biológica > Universidade Nova de Lisboa - 6º Floor (Room 601) > Av. da República, EAN, Apartado 127 > 2781-901 Oeiras, Portugal > Tel. : +351 214469618 /Mobile: +351 96 7562285 > E-mail: machuque at itqb.unl.pt > www: http://www.itqb.unl.pt/~machuque > __________________________________________ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
