[gmx-users] g_dipoles

[Viswanadham Sridhara]

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