[gmx-users] g_dipoles - averaging

[Dommert Florian]

On Thu, 2011-08-04 at 15:49 +0100, Kukol, Andreas wrote: 
> Florian,
> 
> I am not sure, which of the output files of g_current contains the dipole moment for each molecule. Applying g_current to a trajectory of four molecules of asparagin in water gives the following output:
> 

To obtain the dipole moment for every single molecule you have to create
index groups for every single molecule, and the output you are looking
for is the rotational part of M contained in md.xvg
the -eps flag is also not necessary and only required for the
calculation of the dielectric constant. 

/Flo

> g_current -s tpr_200ps.tpr -f xtcIRWhole_100-200ps.xtc -eps 80 -o current.xvg
> (selecting 4 molecules of asparagin from the index group)
> 
> md.xvg
> @    title "Averaged rotational part of M"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "< M\sD\N > (enm)"
> @TYPE xy
> # time	 x	 y 	 z 	 average of M_D^2 	 std.dev
> 0.000	-0.10261	 0.12324	 0.27085	 0.09908	 0.31477
> 0.001	-0.10421	 0.12287	 0.27297	 0.09977	 0.31587
> 0.002	-0.09766	 0.12637	 0.27104	 0.09951	 0.31543
> ...
> 
> dsp.xvg
> @    title "MSD of the squared translational dipole moment M"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "<|M\sJ\N(t)-M\sJ\N(0)|\S2\N > / 6.0*V*k\sB\N*T / Sm\S-1\Nps\S-1\N"
> @TYPE xy
> #Prefactor fit E-H: 1 / 6.0*V*k_B*T: 3.15249e-11
> 0.000	         0
> 0.001	8.70985e-30
> 0.002	1.9936e-29
> ...
> 
> mj.xvg
> @    title "Averaged translational part of M"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "< M\sJ\N > (enm)"
> @TYPE xy
> # time	 x	 y 	 z 	 average of M_J^2 	 std.dev
> 0.000	 0.00001	 0.00000	 0.00000	 0.00000	 0.00001
> 0.001	 0.00001	 0.00000	 0.00000	 0.00000	 0.00001
> ...
> 
> current.xvg was not produced due to:
> ...
> ...
> Average volume V=32.764893 nm^3 at T=300.000000 K
> and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 
> Too less points for a fit.verage volume V=32.764893 nm^3 at T=300.000000 K
> and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 
> Too less points for a fit.
> 
> I am not sure, where to find the dipole moment for each of the four molecules.
> 
> Many thanks
> Andreas
> 
> 
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> > On Behalf Of Dommert Florian
> > Sent: 04 August 2011 12:31
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] g_dipoles - averaging
> > 
> > On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote:
> > > Hello,
> > >
> > > Is there any way to output the dipole moment averaged over all molecules
> > or for each molecule separately (and not the total dipole moment of the
> > simulation box) ?
> > >
> > 
> > Yes, the tool g_current decomposes the total dipole moment into a component
> > in respect to the center of mass of the molecules and a translational term,
> > which is present, if you are dealing with charged species. So, if you
> > prepare a corresponding index file you can derive the average molecular
> > dipole moment for every molecule and finally average the results.
> > 
> > /Flo
> > 
> > > Apparently the dipole autocorrelation function can be obtained as an
> > average over all molecules with the '-corr mol' option, but from the help
> > info it is not clear, how and if the total dipole moment can be obtained in
> > this way (and in which file Mtot.xvg or aver.xvg ?).
> > >
> > > Many thanks
> > > Andreas
> > >
> > 
> > 
> > 
> > --
> > Florian Dommert
> > Dipl. - Phys.
> > 
> > Institute for Computational Physics
> > University Stuttgart
> > 
> > Pfaffenwaldring 27
> > 70569 Stuttgart
> > 
> > EMail: dommert at icp.uni-stuttgart.de
> > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
> > 
> > Tel.: +49 - (0)711 - 68563613
> > Fax.: +49 - (0)711 - 68563658
> -- 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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