Did you get chance to take look at the g_current? why it is -inf (infinity) at the end with -mc option (mc.xvg). > > >> -----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 >
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