Hi Nilesh, I looked at the code and was not able to find a reasonable condition, where the last column of the mc output can contain -inf. The only thing where the normalization would produce something like this is, when the number of frames (nfr) equals the counter in the loop i for the integral calculation. However this is a while loop with the condition while(i<nfr) ( see line 291ff of gmx_current.c. Does this error always occur or only for a certain trajectory? Do you use the whole system as index group, which is necessary?
Unfortunately I have no trr lying around on my own computer. Can you provide me access to a short trajectory, say a few thousand saved frames, including the required top, mdp and gro files such that I can generate a corresponding tpr? /Flo > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Nilesh Dhumal > Sent: Sunday, September 08, 2013 11:55 PM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] g_current > > 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 > > > > -- > 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
