[gmx-users] g_dipoles
David
spoel at xray.bmc.uu.se
Wed Nov 9 22:38:46 CET 2005
On Wed, 2005-11-09 at 15:36 -0500, Viswanadham Sridhara wrote:
> Hello again,
> 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.....
The same way, here is the source code from gmx_dipoles.c (e2d converts e
nm to Debye).
void mol_dip(int k0,int k1,atom_id ma[],rvec x[],t_atom atom[],rvec mu)
{
int k,kk,m;
real q;
clear_rvec(mu);
for(k=k0; (k<k1); k++) {
kk = ma[k];
q = e2d(atom[kk].q);
for(m=0; (m<DIM); m++)
mu[m] += q*x[kk][m];
}
}
>
> --------------------
>
> 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".
> > _______________________________________________
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> > http://www.gromacs.org/mailman/listinfo/gmx-users
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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".
>
>
>
>
> --
> 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
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