[gmx-users] g_current

[Nilesh Dhumal]

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-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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