[gmx-users] g_current

[Florian Dommert]

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at 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-bounces at gromacs.org [mailto:gmx-users-
> >> bounces at gromacs.org] On Behalf Of Nilesh Dhumal
> >> Sent: Monday, July 08, 2013 10:32 PM
> >> To: gmx-users at 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
> >>
> >>
> >>
> >> --
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