AW: AW: AW: [gmx-users] g_current

Mon Feb 25 15:31:04 CET 2013

Hi,

 Can you update your Gromacs version to an actual release and check if the
problem still occurs. It is very strange that the Einstein-Helfand fit gives
0 for sigma and M_J^2.

Cheers,
Flo

-------
Florian Dommert
Dipl. Phys.

Institut für Computerphysik
Universität Stuttgart
Allmandring 3
D-70569 Stuttgart

Tel.: 0711-68563613
Fax: 0711-68563658

> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] Im Auftrag von Nilesh Dhumal
> Gesendet: Montag, 25. Februar 2013 14:00
> An: Discussion list for GROMACS users
> Betreff: Re: AW: AW: [gmx-users] g_current
> 
> Hello,
> 
>  I am using Gromacs VERSION 4.0.7.
> 
> Nilesh
> 
> 
> > Hi,
> >
> >  Which version of gromacs are you using. I am applying this tool also
> > to ILs and it works fine for me in the release-4-5 branch. It is
> > especially strange that you have a rotational dipole moment of zero.
> > However, currently I have no idea where the segfault arises.
> > Especially because you get an output.
> > So
> > what version you are using?
> >
> > Cheers,
> > Flo
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >> bounces at gromacs.org] Im Auftrag von Nilesh Dhumal
> >> Gesendet: Montag, 25. Februar 2013 00:05
> >> An: Discussion list for GROMACS users
> >> Betreff: Re: AW: [gmx-users] g_current
> >>
> >> Hello,
> >>
> >> My system is ionic liquids composed of 128 cation (EMIM) and 128
> >> anion
> > (ethyl
> >> sulfate). I choose system (0) as index group.
> >>
> >> Nilesh
> >>
> >> > Hi,
> >> >
> >> >  Can you be a little bit more specific about your system, and what
> >> > you have chosen as index groups ?
> >> >
> >> > /Flo
> >> >
> >> > -------
> >> > Florian Dommert
> >> > Dipl. Phys.
> >> >
> >> > Institut für Computerphysik
> >> > Universität Stuttgart
> >> > Allmandring 3
> >> > D-70569 Stuttgart
> >> >
> >> > Tel.: 0711-68563613
> >> > Fax: 0711-68563658
> >> >
> >> >> -----Ursprüngliche Nachricht-----
> >> >> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >> >> bounces at gromacs.org] Im Auftrag von Nilesh Dhumal
> >> >> Gesendet: Samstag, 23. Februar 2013 16:17
> >> >> An: gmx-users at gromacs.org
> >> >> Betreff: [gmx-users] g_current
> >> >>
> >> >> Hello,
> >> >>
> >> >> I am calculating the correlation of the rotational and
> >> >> translational
> >> > dipole
> >> >> moment of the system using g_current.
> >> >>
> >> >> I used following command
> >> >>
> >> >> g_current -f md.trr -s md.tpr –mc
> >> >>
> >> >> It crashed with segmental fault.
> >> >> Last frame      15000 time 30000.002
> >> >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11
> >> >>
> >> >>
> >> >> Average translational dipole moment M_J [enm] after 15001 frames
> >> >> (|M|^2):
> >> >> -0.000000 -0.000000 -0.000000 (0.000000)
> >> >>
> >> >>
> >> >> Average molecular dipole moment M_D [enm] after 15001 frames
> (|M|^2):
> >> >> -7.281919 17.954138 5.845435 (490.493744)
> >> >>
> >> >> ********************************************
> >> >>
> >> >> Absolute values:
> >> >>  epsilon=2723.718750
> >> >>  <M_D^2> , <M_J^2>, <(M_J*M_D)^2>:  (490.493744, 0.000000,
> >> >> -0.000003)
> >> >>
> >> >> ********************************************
> >> >>
> >> >>
> >> >> Fluctuations:
> >> >>  epsilon=450.336090
> >> >>
> >> >>
> >> >>  deltaM_D , deltaM_J, deltaM_JD:  (80.947235, 0.000000, 0.000000)
> >> >>
> >> >> ********************************************
> >> >>
> >> >> Static dielectric constant using integral and fluctuations:
> >> >> 450.336090
> >> >>
> >> >>  < M_JM_D > via integral:  -0.000
> >> >>
> >> >> ***************************************************
> >> >>
> >> >> Average volume V=42.031509 nm^3 at T=300.000000 K and
> >> >> corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975
> >> >>
> >> >> Start fit at 98.000008 ps (100.000000).
> >> >> End fit at 398.000031 ps (400.000000).
> >> >>
> >> >> Einstein-Helfand fit to the MSD of the translational dipole moment
> >> >> yields:
> >> >>
> >> >> sigma=0.0000
> >> >> translational fraction of M^2: 0.0000 Dielectric constant using EH:
> >> >> 2723.7188 Segmentation fault
> >> >>
> >> >>
> >> >> Can you whats the problem?
> >> >>
> >> >> Nilesh
> >> >>
> >> >> --
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> >> >
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> 
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