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
