AW: AW: AW: AW: AW: [gmx-users] g_current
Florian Dommert
dommert at icp.uni-stuttgart.de
Wed Feb 27 09:35:21 CET 2013
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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