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

Wed Feb 27 17:26:28 CET 2013

Hi,

 Have you done a similar analysis with another IL system or is it the first
time you use g_current? Currently I am not able to figure out what the
problem is. However 2ps saving interval is quite long for such a kind of
analysis. A zero value of the translational dipole moment hints to neutral
molecules which should not be the case for your system. What is written in
the output of mj.xvg. Is filled with zeros?

/Flo

> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] Im Auftrag von Nilesh Dhumal
> Gesendet: Mittwoch, 27. Februar 2013 15:26
> An: Discussion list for GROMACS users
> Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current
> 
> Hello,
> 
> Yes. Segfault is solved. I saving velocites and coordinates at 2 ps.
> 
> Nilesh
> 
> > Hi,
> >
> >  At least the segfault is solved. However, the zero output of M_J for
> > your IL system is really strange. I'm thinking about a reason, but I
> > am currently not able to find one. How often do you write out
> > velocities and coordinates in your trr file?
> >
> > /Flo
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >> bounces at gromacs.org] Im Auftrag von Nilesh Dhumal
> >> Gesendet: Dienstag, 26. Februar 2013 17:50
> >> An: Discussion list for GROMACS users
> >> Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current
> >>
> >> Hello,
> >>
> >> I didn't get any segmental fault if I use Gromacs Version 4.5.5.
> >>
> >>  g_current -f md.trr -s md.tpr -mc
> >>
> >> Program didn't write the mc.xvg
> >>
> >> Average translational dipole moment is zero.
> >>
> >> Average translational dipole moment M_J [enm] after 15001 frames
> >> (|M|^2):
> >> -0.000000 -0.000000 -0.000000 (0.000000)
> >>
> >> Can you tell where is the problem?
> >>
> >> Nilesh
> >>
> >> > Hi,
> >> > I am using the release branch of 4.5.
> >> >
> >> > /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 15:35
> >> >> An: Discussion list for GROMACS users
> >> >> Betreff: Re: AW: AW: AW: [gmx-users] g_current
> >> >>
> >> >> Hello,
> >> >>
> >> >> Thanks.
> >> >>
> >> >> I will update Gromacs version. Can you tell which version you are
> >> >> using ?
> >> >>
> >> >> Nilesh
> >> >>
> >> >> > 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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