Hi, I am using the release branch of 4.5. /Flo
------- Florian Dommert Dipl. Phys. Institut für Computerphysik Universität Stuttgart Allmandring 3 D-70569 Stuttgart Tel.: 0711-68563613 Fax: 0711-68563658 > -----Ursprüngliche Nachricht----- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > Gesendet: Montag, 25. Februar 2013 15:35 > An: Discussion list for GROMACS users > Betreff: Re: AW: AW: AW: [gmx-users] g_current > > Hello, > > Thanks. > > I will update Gromacs version. Can you tell which version you are using ? > > Nilesh > > > Hi, > > > > Can you update your Gromacs version to an actual release and check if > > the problem still occurs. It is very strange that the Einstein-Helfand > > fit gives > > 0 for sigma and M_J^2. > > > > Cheers, > > Flo > > > > ------- > > Florian Dommert > > Dipl. Phys. > > > > Institut für Computerphysik > > Universität Stuttgart > > Allmandring 3 > > D-70569 Stuttgart > > > > Tel.: 0711-68563613 > > Fax: 0711-68563658 > > > >> -----Ursprüngliche Nachricht----- > >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > >> Gesendet: Montag, 25. Februar 2013 14:00 > >> An: Discussion list for GROMACS users > >> Betreff: Re: AW: AW: [gmx-users] g_current > >> > >> Hello, > >> > >> I am using Gromacs VERSION 4.0.7. > >> > >> Nilesh > >> > >> > >> > Hi, > >> > > >> > Which version of gromacs are you using. I am applying this tool > >> > also to ILs and it works fine for me in the release-4-5 branch. It > >> > is especially strange that you have a rotational dipole moment of zero. > >> > However, currently I have no idea where the segfault arises. > >> > Especially because you get an output. > >> > So > >> > what version you are using? > >> > > >> > Cheers, > >> > Flo > >> > > >> >> -----Ursprüngliche Nachricht----- > >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > >> >> Gesendet: Montag, 25. Februar 2013 00:05 > >> >> An: Discussion list for GROMACS users > >> >> Betreff: Re: AW: [gmx-users] g_current > >> >> > >> >> Hello, > >> >> > >> >> My system is ionic liquids composed of 128 cation (EMIM) and 128 > >> >> anion > >> > (ethyl > >> >> sulfate). I choose system (0) as index group. > >> >> > >> >> Nilesh > >> >> > >> >> > Hi, > >> >> > > >> >> > Can you be a little bit more specific about your system, and > >> >> > what you have chosen as index groups ? > >> >> > > >> >> > /Flo > >> >> > > >> >> > ------- > >> >> > Florian Dommert > >> >> > Dipl. Phys. > >> >> > > >> >> > Institut für Computerphysik > >> >> > Universität Stuttgart > >> >> > Allmandring 3 > >> >> > D-70569 Stuttgart > >> >> > > >> >> > Tel.: 0711-68563613 > >> >> > Fax: 0711-68563658 > >> >> > > >> >> >> -----Ursprüngliche Nachricht----- > >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > >> >> >> Gesendet: Samstag, 23. Februar 2013 16:17 > >> >> >> An: gmx-users@gromacs.org > >> >> >> Betreff: [gmx-users] g_current > >> >> >> > >> >> >> Hello, > >> >> >> > >> >> >> I am calculating the correlation of the rotational and > >> >> >> translational > >> >> > dipole > >> >> >> moment of the system using g_current. > >> >> >> > >> >> >> I used following command > >> >> >> > >> >> >> g_current -f md.trr -s md.tpr mc > >> >> >> > >> >> >> It crashed with segmental fault. > >> >> >> Last frame 15000 time 30000.002 > >> >> >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 > >> >> >> > >> >> >> > >> >> >> Average translational dipole moment M_J [enm] after 15001 > >> >> >> frames > >> >> >> (|M|^2): > >> >> >> -0.000000 -0.000000 -0.000000 (0.000000) > >> >> >> > >> >> >> > >> >> >> Average molecular dipole moment M_D [enm] after 15001 frames > >> (|M|^2): > >> >> >> -7.281919 17.954138 5.845435 (490.493744) > >> >> >> > >> >> >> ******************************************** > >> >> >> > >> >> >> Absolute values: > >> >> >> epsilon=2723.718750 > >> >> >> <M_D^2> , <M_J^2>, <(M_J*M_D)^2>: (490.493744, 0.000000, > >> >> >> -0.000003) > >> >> >> > >> >> >> ******************************************** > >> >> >> > >> >> >> > >> >> >> Fluctuations: > >> >> >> epsilon=450.336090 > >> >> >> > >> >> >> > >> >> >> deltaM_D , deltaM_J, deltaM_JD: (80.947235, 0.000000, > >> >> >> 0.000000) > >> >> >> > >> >> >> ******************************************** > >> >> >> > >> >> >> Static dielectric constant using integral and fluctuations: > >> >> >> 450.336090 > >> >> >> > >> >> >> < M_JM_D > via integral: -0.000 > >> >> >> > >> >> >> *************************************************** > >> >> >> > >> >> >> Average volume V=42.031509 nm^3 at T=300.000000 K and > >> >> >> corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975 > >> >> >> > >> >> >> Start fit at 98.000008 ps (100.000000). > >> >> >> End fit at 398.000031 ps (400.000000). > >> >> >> > >> >> >> Einstein-Helfand fit to the MSD of the translational dipole > >> >> >> moment > >> >> >> yields: > >> >> >> > >> >> >> sigma=0.0000 > >> >> >> translational fraction of M^2: 0.0000 Dielectric constant using > >> EH: > >> >> >> 2723.7188 Segmentation fault > >> >> >> > >> >> >> > >> >> >> Can you whats the problem? > >> >> >> > >> >> >> Nilesh > >> >> >> > >> >> >> -- > >> >> >> 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 > >> >> > > >> >> > > >> >> > >> >> > >> >> -- > >> >> 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 > >> > > >> > > >> > >> > >> -- > >> 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 > > > > > > > -- > 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? 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