AW: AW: AW: AW: AW: [gmx-users] g_current
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Wed Feb 27 15:25:32 CET 2013
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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