> -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Nilesh Dhumal > Sent: Tuesday, July 09, 2013 5:06 AM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] g_current > > Thanks for reply. > > Still I have a question why it is -inf (infinity) at the end.
This is a good question. At the moment, the only thing I can imagine is a faulty normalization, because the value of the integral at t=0 equals always zero. However, if you integrate the first row with another tool, such as g_analyze for example, the same values as in the second row show appear. As soon as I have some time left, I will take a look at the code and report back. /Flo > > Nilesh > > > Hi, > > > > I would say the problem is too less statistics. In the paper where the > > tool > > was introduced, a simulation of 100ns has been performed in order to > > achieved sufficient sampling. > > > > The order of magnitude is given due to the units. > > > > Simulate for a longer time to get rid of the noise. Calculating these kind > > of correlations functions is really not a simple task. > > > > Schroeder et al. have published an article about fitting of dielectric > > spectra for ionic liquids, where this problem is discussed in detail. > > > > Cheers, > > Flo > > > >> -----Original Message----- > >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal > >> Sent: Monday, July 08, 2013 10:32 PM > >> To: gmx-users@gromacs.org > >> Subject: [gmx-users] g_current > >> > >> Hello, > >> I am calculating the correlation of rotational and translation dipole > >> moment of ionic liquids. I run the 1 ns simulation and saved the > >> trajectory at 1 fs. > >> > >> g_current -f md.trr -s md.tpr -n index.ndx -mc > >> > >> I selected "system" group. > >> > >> Here I pasted the initial j(t) vales and the final value is infinity. > >> > >> # This file was created Sun Jul 7 20:51:59 2013 > >> # by the following command: > >> # g_current -f md.trr -s md.tpr -e 10.0 -mc > >> # > >> # g_current is part of G R O M A C S: > >> # > >> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon > >> # > >> @ title "M\sD\N - current autocorrelation function" > >> @ xaxis label "Time (ps)" > >> @ yaxis label "< M\sD\N (0)\c7\CJ(t) > (e nm/ps)\S2" > >> @TYPE xy > >> # time M_D(0) J(t) acf Integral acf > >> 0.000 -5.20584e-15 0 > >> 0.001 -6.97466e-15 -1.42702e-17 > >> 0.002 -6.97511e-15 -5.25081e-17 > >> 0.003 -6.97474e-15 -9.07484e-17 > >> 0.004 -6.97391e-15 -1.28987e-16 > >> > >> > >> > >> Why final value is infinity? If I do autocorrelation function of these > >> values, I get all values 0. > >> > >> Why J(t)values are in range of e-15? > >> > >> 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
