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

Fri Mar 1 15:02:31 CET 2013

Hi,
 Now I've tested the version of g_current in 4.6 and for me it works fine.
/Flo

> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] Im Auftrag von Florian Dommert
> Gesendet: Mittwoch, 27. Februar 2013 18:46
> An: 'Discussion list for GROMACS users'
> Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
> 
> > -----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
> > >> >> >> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > >> >> >> >> posting!
> > >> >> >> >> >> >> * Please don't post (un)subscribe requests to the
list.
> > >> >> >> >> >> >> Use the www
> > >> >> >> >> >> > interface or
> > >> >> >> >> >> >> send it to gmx-users-request at gromacs.org.
> > >> >> >> >> >> >> * 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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> > >> >> >> > --
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> > > posting!
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gmx-users-request at gromacs.org.
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> > >> >> >>
> > >> >> >>
> > >> >> >> --
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> > >> posting!
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> > >> >> > --
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> > >> >> >
> > >> >>
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> > >> >
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> > >>
> > >>
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