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

Sun Mar 3 00:51:29 CET 2013

Hello,

I run a 500ps simulation and save the trajectory each 3fs.

g_current work till 498ps and later it shows -nan.

Can you tell where is the problem

Nilesh

> 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
>> > >> >> >> >> >> >>
>> > >> >> >> >> >> >> --
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>