[gmx-users] diffusion coefficient of oxygen molecule
Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient of oxygen molecule
Sunil Thapa skrev: Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I want to reproduce this value. In your experience, which model of water would give the closer value. I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding potential has been taken to be harmonic. Any knowledge of related literature would be helpful because I could not find by googling. Your idea will really help me. Neal Hi, I do know that there are finite size effects that affects the diffusion coefficient, so you should make sure you use a big enough box. Furthermore, for water polarizability has an impact on the diffusion coefficient, so if you want to reproduce experimental values, consider using a polarizable model. -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] diffusion coefficient of oxygen molecule
Hi, If i remember correctly SPC/E water might be worth trying. There is plenty of research paper in this field. Try this paper http://pubs.acs.org/doi/abs/10.1021/jp003020w Also P,T coupling have effects on Diffusion Coeff. amit On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa wrote: > Respected experts > I want to calculate the self diffusion cofficient of an oxygen molecule in > water. The experimental value in the literature is found to be 2.5 x 10-9 > nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off > Lennard Jones interaction between water and oxygen. I want to reproduce this > value. In your experience, which model of water would give the closer value. > I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units > and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding > potential has been taken to be harmonic. Any knowledge of related literature > would be helpful because I could not find by googling. > > Your idea will really help me. > Neal > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
