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

Wed Mar 6 17:18:30 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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