[gmx-users] g_dipoles

[David]

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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