[gmx-users] g_dipoles

Wed Nov 9 21:36:55 CET 2005

Hello again,
Thanks David for the quick response, but i have few doubts with the output
files of g_dipoles.....
I am just pasting files, so that it will be easy for everyone to
understand.....but only a part of the files though,
------
# This file was created by g_dipoles_AMD32
# which is part of G R O M A C S:
# GROningen MAchine for Chemical Simulation
# All this happened at: Wed Nov 9 13:49:28 2005
#
@ title "Total dipole moment of the simulation box vs. time"
@ xaxis label "Time (ps)"
@ yaxis label "Total Dipole Moment (Debye)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "M\sx \N"
@ s1 legend "M\sy \N"
@ s2 legend "M\sz \N"
@ s3 legend "|M\stot \N|"
0 2.64626166e+02 1.16440350e+03 -8.75332770e+01 1.19729888e+03
4 9.62820668e+02 1.12993143e+03 -2.29642353e+02 1.50216653e+03
8 1.04575875e+03 6.88685425e+02 -2.78564322e+02 1.28276929e+03

------
# This file was created by g_dipoles_AMD32
# which is part of G R O M A C S:
# Gromacs Runs One Microsecond At Cannonball Speeds
# All this happened at: Wed Nov 9 13:52:51 2005
#
@ title "Total dipole moment"
@ xaxis label "Time (ps)"
@ yaxis label "D"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "< |M|\S2\N >"
@ s1 legend "< |M| >\S2\N"
@ s2 legend "< |M|\S2\N > - < |M| >\S2\N"
@ s3 legend "< |M| >\S2\N / < |M|\S2\N >"
0 1.434e+06 1.434e+06 1.921e-11 1.000e+00
4 1.845e+06 1.718e+06 1.272e+05 9.310e-01
8 1.779e+06 1.602e+06 1.762e+05 9.009e-01
------

The first two vectors < |M|\S2\N > and < |M| >\S2\N" are assumed to be equal
in the very first time step, but from 4ps in th is case, they are different,
can anyone tell me how they are calculated.
I understand how they are calculated at t-0,
sum[(M\sx \N)^2 (M\sy \N )^2 (M\sz \N)^2] and it is made equal for both <
|M|\S2\N > and < |M| >\S2\N", so that their ratio is 1, 4th column in second
file........
But how are they calculated for t =4 ...and so on.....

--------------------

I hope I am clear this time....
Thanks in advance

Viswam..

On 11/9/05, Viswanadham Sridhara <muta.mestri at gmail.com> wrote:
>
> Hello David,
> Then why are the files 11.xvg and 111.xvg same as first half of 1.xvg and
> the second half of 1.xvg respectively, in other words the total dipole
> moment of the frames for the whole trajectory is same as when calculated
> separately for the first and second halves and concatenated, but not the
> dipole plus fluctuations...........(22.xvg and 222.xvg are different
> compared to 2.xvg)...
> Thanks,
>
>
> On 11/9/05, David <spoel at xray.bmc.uu.se> wrote:
> >
> > On Wed, 2005-11-09 at 14:38 -0500, Viswanadham Sridhara wrote:
> > > Hello Everyone,
> > > Can anyone explain me how g_dipoles exactly work?
> > > I am just briefly explaining what I did.
> > > a) I took the whole trajectory and tried to find dipole moment, --
> > > >full.xvg (This is with option -o)
> > > b)then i divided the whole trajectory into two parts and tried to find
> > > the dipole moment, first half-->fh.xvg and second half sh.xvg.
> > > Obviously fh.xvg and sh.xvg combined is equal to full.xvg.
> > >
> > > But, when i use option -a in g_dipoles, and tried to find <Mu>^2 -
> > > <Mu^2> for the whole trajectory, the n umbers I found are different
> > > for the trajectory when divided into two parts.
> > >
> > > -------------------
> > > g_dipoles -f full.gro -s dppc.tpr -o 1 -a 2 -mu 2.273 -mumax 5.0 -
> > > epsilonRF 78.5
> > > g_dipoles -f firsthalf.gro -s dppc.tpr -o 11 -a 22 -mu 2.273 -mumax
> > > 5.0 -epsilonRF 78.5
> > > g_dipoles -f secondhalf.gro -s dppc.tpr -o 111 -a 222 -mu 2.273 -mumax
> > > 5.0 -epsilonRF 78.5
> > > -------------------------------------
> > >
> > > In other words, concatenating 11 and 111 gives me 1.xvg, but not with
> > > 22 and 222......
> > > How does Gromacs calculate <Mu>^2 and <Mu^2>......
> > Mu = Sum q R
> > where Mu and R are vectors.
> >
> > Obviously if you compare two single coordinate files the results will be
> >
> > different.
> >
> > > Thanks in advance,
> > > Viswam.
> > >
> > >
> > >
> > > --
> > > Viswanadham Sridhara,
> > > Graduate Research Assistant,
> > > Old Dominion University, "VIRGINIA".
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org .
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel<http://xray.bmc.uu.se/%7Espoel>
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
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>
>
>
> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA".
>

--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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