> -----Ursprüngliche Nachricht----- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > Gesendet: Mittwoch, 27. Februar 2013 17:38 > An: Discussion list for GROMACS users > Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current > > Hello, > > I am using g_current for first time. Now I am running additional simulation and I > will save trajectory at 2 fs. > > Is it possible to calculate contribution of rotational and translation to dipole > moment simultaneously with the simulation instead of saving the trajectory at > each 2fs? >
Hi, This is one of my majors on my to do list, but currently not possible. I think a saving frequency of 0.05 ps should be fine. /Flo > Nilesh > > > Hi, > > > > Have you done a similar analysis with another IL system or is it the > > first time you use g_current? Currently I am not able to figure out > > what the problem is. However 2ps saving interval is quite long for > > such a kind of analysis. A zero value of the translational dipole > > moment hints to neutral molecules which should not be the case for > > your system. What is written in the output of mj.xvg. Is filled with > > zeros? > > > > /Flo > > > > > >> -----Ursprüngliche Nachricht----- > >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > >> Gesendet: Mittwoch, 27. Februar 2013 15:26 > >> An: Discussion list for GROMACS users > >> Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current > >> > >> Hello, > >> > >> Yes. Segfault is solved. I saving velocites and coordinates at 2 ps. > >> > >> Nilesh > >> > >> > Hi, > >> > > >> > At least the segfault is solved. However, the zero output of M_J > >> > for your IL system is really strange. I'm thinking about a reason, > >> > but I am currently not able to find one. How often do you write out > >> > velocities and coordinates in your trr file? > >> > > >> > /Flo > >> > > >> >> -----Ursprüngliche Nachricht----- > >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > >> >> Gesendet: Dienstag, 26. Februar 2013 17:50 > >> >> An: Discussion list for GROMACS users > >> >> Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current > >> >> > >> >> Hello, > >> >> > >> >> I didn't get any segmental fault if I use Gromacs Version 4.5.5. > >> >> > >> >> g_current -f md.trr -s md.tpr -mc > >> >> > >> >> Program didn't write the mc.xvg > >> >> > >> >> Average translational dipole moment is zero. > >> >> > >> >> Average translational dipole moment M_J [enm] after 15001 frames > >> >> (|M|^2): > >> >> -0.000000 -0.000000 -0.000000 (0.000000) > >> >> > >> >> Can you tell where is the problem? > >> >> > >> >> Nilesh > >> >> > >> >> > 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? 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? 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
