[gmx-users] g_dipoles - averaging

[Kukol, Andreas]

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:

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