Hello, I run a 500ps simulation and save the trajectory each 3fs.
g_current work till 498ps and later it shows -nan. Can you tell where is the problem Nilesh > Hi, > Now I've tested the version of g_current in 4.6 and for me it works fine. > /Flo > >> -----Ursprüngliche Nachricht----- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Florian Dommert >> Gesendet: Mittwoch, 27. Februar 2013 18:46 >> An: 'Discussion list for GROMACS users' >> Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current >> >> > -----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 > > -- > 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
