[gmx-users] g_dipoles

Tue Nov 15 20:33:11 CET 2005

Thanks David.
One more quick question.
g_dipoles takes the molecule number unlike atom number for g_density.
So if I ran a simulation, is there any way out later to divide the molecule
into 2 seperate entities and find the dipole moment for these 2 entities.
In other words if i ran the simulation with one kind of molecule which has a
head and tail, and later I want to seperately calculate the dipole moment
for the head and for the tail, is there any other way instead of re-running
the entire simulation by dividing these two groups.......
(((( A has B and C entities, I want to find the dipole moment of B and C
separately. ))))
I hope my question is clear...
Thanks,
Viswam.

On 11/10/05, David <spoel at xray.bmc.uu.se> wrote:
>
> 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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> > > --
> > > 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
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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
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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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