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

Wed Feb 27 18:45:53 CET 2013

> -----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 17:38
> An: Discussion list for GROMACS users
> Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
> 
> Hello,
> 
> I am using g_current for first time. Now I am running additional
simulation and I
> will save trajectory at 2 fs.
> 
> Is it possible to calculate contribution of rotational and translation to
dipole
> moment simultaneously with the simulation instead of saving the trajectory
at
> each 2fs?
> 

Hi,

 This is one of my majors on my to do list, but currently not possible. I
think a saving frequency of 0.05 ps should be fine. 

/Flo

> Nilesh
> 
> > 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
> >> >> >> >> >> >>
> >> >> >> >> >> >> --
> >> >> >> >> >> >> gmx-users mailing list    gmx-users at gromacs.org
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> >> >> >> >> >> >> Use the www
> >> >> >> >> >> > interface or
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> >> >> >> >> >> >> * Can't post? Read
> >> >> >> >> >> >> http://www.gromacs.org/Support/Mailing_Lists
> >> >> >> >> >> >
> >> >> >> >> >> > --
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> >> >> >> >> >> >
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> --
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> >> >> >> >> >
> >> >> >> >> > --
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> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
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> >> >> posting!
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> >> >> >> >> the www
> >> >> >> > interface or
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> >> >> >> >
> >> >> >> > --
> >> >> >> > gmx-users mailing list    gmx-users at gromacs.org
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> >> >> >> > * Please search the archive at
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> > posting!
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> >> >> >> >
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >> --
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> >> posting!
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> >> >> >> www
> >> >> > interface or
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> >> >> >
> >> >> > --
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> >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> >> > * Please search the archive at
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posting!
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> >> >> >
> >> >> >
> >> >>
> >> >> --
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> >> >
> >> > --
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> >> >
> >>
> >>
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> >> gmx-users mailing list    gmx-users at gromacs.org
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> >
> > --
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> >
> >
> 
> 
> --
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