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? 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: [email protected] [mailto:gmx-users- >> [email protected]] 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: [email protected] [mailto:gmx-users- >> >> [email protected]] 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: [email protected] [mailto:gmx-users- >> >> >> [email protected]] 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: [email protected] [mailto:gmx-users- >> >> >> >> [email protected]] 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: [email protected] [mailto:gmx-users- >> >> >> >> >> [email protected]] 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: [email protected] [mailto:gmx-users- >> >> >> >> >> >> [email protected]] Im Auftrag von Nilesh Dhumal >> >> >> >> >> >> Gesendet: Samstag, 23. Februar 2013 16:17 >> >> >> >> >> >> An: [email protected] >> >> >> >> >> >> 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 [email protected] >> >> >> >> >> >> 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 [email protected]. >> >> >> >> >> >> * Can't post? Read >> >> >> >> >> >> http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> > >> >> >> >> >> > -- >> >> >> >> >> > gmx-users mailing list [email protected] >> >> >> >> >> > 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 >> >> [email protected]. >> >> >> >> >> > * Can't post? Read >> >> >> >> >> > http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> gmx-users mailing list [email protected] >> >> >> >> >> 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 [email protected]. >> >> >> >> >> * Can't post? Read >> >> >> >> >> http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> > >> >> >> >> > -- >> >> >> >> > gmx-users mailing list [email protected] >> >> >> >> > 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 >> [email protected]. >> >> >> >> > * Can't post? Read >> >> >> >> > http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> gmx-users mailing list [email protected] >> >> >> >> 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 [email protected]. >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > >> >> >> > -- >> >> >> > gmx-users mailing list [email protected] >> >> >> > 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 [email protected]. >> >> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> >> -- >> >> >> gmx-users mailing list [email protected] >> >> >> 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 [email protected]. >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > >> >> > -- >> >> > gmx-users mailing list [email protected] >> >> > 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 [email protected]. >> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > >> >> > >> >> >> >> -- >> >> gmx-users mailing list [email protected] >> >> 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 [email protected]. >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > -- >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
