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

Wed Feb 27 17:37:57 CET 2013

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?

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
>> >> >> >> >> >>
>> >> >> >> >> >> --
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>> >> >> >> posting!
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>> >> >> >> >> >> 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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>> >> >
>> >> >
>> >>
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>> >
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>> >
>>
>>
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>
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>