Dear All, I've found that the dielectric constant of pure SPC water according to g_dipoles is only 3.94, which is obviously wrong! I simulated the box of ~1500 SPC waters at 325 K and computed epsilon with
g_dipoles -temp 325 That's what I get: Finite system Kirkwood g factor G_k = 0.190603 Infinite system Kirkwood g factor g_k = 0.143163 Epsilon = 3.94756 After some googling I've found that eps=65 for SPC model. So, what is wrong? Is there any other way of computing epsilon? Sincerely, Semen ----- Original Message ---- From: David van der Spoel <sp...@xray.bmc.uu.se> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wednesday, December 24, 2008 6:01:38 PM Subject: Re: [gmx-users] g_dipoles questions Semen Esilevsky wrote: > Dear David, > > Thank you for reply! However there are still some question: > > >>> Dear All, >>> I have few questions about g_dipoles, which are not explained in the manual: >>> 1) What method is used to calculate the epsilon? Is there a reference which >>> can be cited? Is it suitable for water solutions? > >> In principle it is suitable for solutions of neutral molecules only. > > So, it should work for SPC water for example? yes. > I'm confused by the phrase in the man page "you can compute e.g. the > dielectric constant for low dielectric media". What is "low"? Does it mean > that the method works for, say, benzene but not for water? anything of neutral molecules. > >> The references are to Neuman papers from the 1980s. > > Could you please give a little bit more detailed citation? Neuman is a > widespread name and 1980s is 10 years... At least a title or some keywords > are needed to find these papers. > check my 1998 JCP paper, the ref is given in g_dipoles. > Sincerely, > Semen > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
