Dear David, Thanks for your reply. I have other questions when calculating frequency dependent dielectric constants through g_dielectric.
1. After using " g_dipoles -corr mol " command to get the dipcorr.xvg, if I uesd " g_dielectric " program, the error is as following. ================ Fatal error: nparm = 0 in file expfit.c, line 465 ========================if I used " g_dielectric -eint 50 -bfit 5 -efit 100 -ffn exp ", then the error is: ================ nbegin = 50, x[nbegin] = 5, tbegin = 5 Step chi^2 Lambda A1 A2 A3 Segmentation Fault================ 2. When I read the manul about g_dielectric, I have a question about the output file " epsw.xvg ". In the manul, it discribs " The second file contains the real and imaginary parts of the frequency-dependent dielectric constant ". How can I get the real parts of the frequency-dependent dielectric constant only ? ( just like the fig. 2. the frequency dependence of the dielectric constant in your papaer J. Chem. Phys. 108 (1998) pp. 10220-10230 ) I appreciate your help. Thanks a lot! ------------------ 原始邮件 ------------------ 发件人: "spoel";<sp...@xray.bmc.uu.se>; 发送时间: 2014年5月30日(星期五) 下午2:11 收件人: "gmx-users"<gmx-us...@gromacs.org>; 主题: Re: [gmx-users] dielectric constant of water by gromacs On 2014-05-30 07:39, Harshkumar Singh wrote: > Can you please describe how to use pme or any other reference? coulombtype = PME in your mdp file. > > > On Thu, May 29, 2014 at 3:40 AM, David van der Spoel <sp...@xray.bmc.uu.se> > wrote: > >> On 2014-05-29 06:07, 来者可追 wrote: >> >>> Dear David, >>> I have a problem when simulating the dielectric constant of water >>> according to g_dipoles.I used the water file in "tutor"(216 SPC waters), >>> when I write the program "g_dipoles", the result is as following, why >>> not Epsilon about 65? >>> >>> ================================= >>> Finite system Kirkwood g factor G_k = 0.163272 >>> Infinite system Kirkwood g factor g_k = 0.123058 >>> >>> Epsilon = 3.83011 >>> ================================= >>> >>> >> Did you use PME? In that case it should work. >> If you used a cut-off you have to redo the simulation. >> >> >> >>> I cannot understand " you have to give extr options, depending on how >>> you did the simulation. g_dipoles -h (hint look at the epsilonRF >>> option). If you used a cut-off then you will not get the right >>> dielectric. " ( >>> https://www.mail-archive.com/gmx-users%40gromacs.org/msg18306.html ) Can >>> you explain it more for me? Thank you so much! >>> >>> >>> Sincerely, >>> LiBin >>> >>> >>> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell & Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.