[gmx-users] g_dipoles
David
spoel at xray.bmc.uu.se
Thu Nov 10 17:53:07 CET 2005
On Thu, 2005-11-10 at 08:51 -0500, Viswanadham Sridhara wrote:
> Hi again,
> Is < |M| >\S2\N intentionally made equal to < |M|\S2\N > for t=0? I
> ask this question because, the difference of these two terms is almost
> zero in every calculation. I am not able to understand exactly how
> each term is calculated, I understand how epsilon, kirkwood factor,
> moments in each direction and total moment are calculated, but I dont
> exactly understand how these fluctuations are calculated.......
> Hope someone clarifies to me briefly how they are calculated at t =0
> and for t = 0 + of the simulation.
For a single step this is by definition correct. Note that M is a vector
of length 3.
> Thanks in advance,
> Viswam.
>
> On 11/9/05, David <spoel at xray.bmc.uu.se> wrote:
> 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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> > > gmx-users at gromacs.org
> > >
> 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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> >
> >
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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
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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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> ++++++++++
>
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>
>
> --
> 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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