Thanks David.<br>
One more quick question.<br>
g_dipoles takes the molecule number unlike atom number for g_density.<br>
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.<br>
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.......<br>
(((( A has B and C entities, I want to find the
dipole moment of B and C separately. ))))<br>
I hope my question is clear...<br>
Thanks,<br>
Viswam.<br><br><div><span class="gmail_quote">On 11/10/05, <b class="gmail_sendername">David</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Thu, 2005-11-10 at 08:51 -0500, Viswanadham Sridhara wrote:<br>> Hi again,<br>> Is < |M| >\S2\N intentionally made equal to < |M|\S2\N > for t=0? I<br>> ask this question because, the difference of these two terms is almost
<br>> zero in every calculation. I am not able to understand exactly how<br>> each term is calculated, I understand how epsilon, kirkwood factor,<br>> moments in each direction and total moment are calculated, but I dont
<br>> exactly understand how these fluctuations are calculated.......<br>> Hope someone clarifies to me briefly how they are calculated at t =0<br>> and for t = 0 + of the simulation.<br>For a single step this is by definition correct. Note that M is a vector
<br>of length 3.<br><br><br>> Thanks in advance,<br>> Viswam.<br>><br>> On 11/9/05, David <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>> On Wed, 2005-11-09 at 15:36 -0500, Viswanadham Sridhara wrote:
<br>> > Hello again,<br>><br>> > The first two vectors < |M|\S2\N > and < |M| >\S2\N" are<br>> assumed to be<br>> > equal in the very first time step, but from 4ps in th is
<br>> case, they<br>> > are different, can anyone tell me how they are calculated.<br>> > I understand how they are calculated at t-0,<br>> > sum[(M\sx \N)^2 (M\sy \N )^2 (M\sz \N)^2] and it is made
<br>> equal for<br>>
> both < |M|\S2\N > and < |M| >\S2\N", so that their
ratio is<br>> 1, 4th<br>> > column in second file........<br>> > But how are they calculated for t =4 ...and so on.....<br>><br>> The same way, here is the source code from gmx_dipoles.c (e2d
<br>> converts e<br>> nm to Debye).<br>><br>> void mol_dip(int k0,int k1,atom_id ma[],rvec x[],t_atom atom<br>> [],rvec mu)<br>> {<br>> int k,kk,m;<br>
> real q;<br>><br>> clear_rvec(mu);<br>> for(k=k0; (k<k1); k++) {<br>> kk = ma[k];<br>> q = e2d(atom[kk].q);<br>> for(m=0; (m<DIM); m++)
<br>> mu[m] += q*x[kk][m];<br>> }<br>> }<br>><br>> ><br>> > --------------------<br>> ><br>> > I hope I am clear this time....
<br>> > Thanks in advance<br>> ><br>> > Viswam..<br>> ><br>> ><br>> ><br>> ><br>> > On 11/9/05, Viswanadham Sridhara <
<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</a>><br>> wrote:<br>> > Hello David,<br>>
> Then why are the
files 11.xvg and 111.xvg same as<br>> first half<br>>
> of 1.xvg and the
second half of 1.xvg respectively,<br>> in other<br>>
> words the total
dipole moment of the frames for the<br>> whole<br>>
> trajectory is same
as when calculated separately for<br>> the first<br>>
> and second halves
and concatenated, but not the<br>> dipole plus<br>>
>
fluctuations...........(22.xvg and 222.xvg are<br>> different<br>> > compared to 2.xvg)...<br>> > Thanks,<br>> ><br>> ><br>> >
<br>>
> On 11/9/05, David
<<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>>
>
On Wed, 2005-11-09 at 14:38 -0500,<br>> Viswanadham<br>>
>
Sridhara wrote:<br>>
>
> Hello Everyone,<br>>
>
> Can anyone explain me how g_dipoles<br>> exactly work?<br>>
>
> I am just briefly explaining what I did.<br>>
>
> a) I took the whole trajectory and tried<br>> to find<br>>
>
dipole moment, --<br>>
>
> >full.xvg (This is with option -o)<br>>
>
> b)then i divided the whole trajectory into<br>> two parts<br>>
>
and tried to find<br>>
>
> the dipole moment, first half-->fh.xvg and<br>> second<br>>
>
half sh.xvg.<br>>
>
> Obviously fh.xvg and sh.xvg combined is<br>> equal to<br>>
>
full.xvg.<br>>
>
><br>>
>
> But, when i use option -a in g_dipoles,<br>> and tried to<br>>
>
find <Mu>^2 -<br>>
>
> <Mu^2> for the whole trajectory, the n<br>> umbers I<br>>
>
found are different<br>>
>
> for the trajectory when divided into two<br>> parts.<br>>
>
><br>>
>
> -------------------<br>>
>
> g_dipoles -f full.gro -s dppc.tpr -o 1 -a<br>> 2 -mu<br>>
>
2.273 -mumax 5.0 -<br>>
>
> epsilonRF 78.5<br>>
>
> g_dipoles -f firsthalf.gro -s dppc.tpr -o<br>> 11 -a 22 -<br>>
>
mu 2.273 -mumax<br>>
>
> 5.0 -epsilonRF 78.5<br>>
>
> g_dipoles -f secondhalf.gro -s dppc.tpr -o<br>> 111 -a<br>>
>
222 -mu 2.273 -mumax<br>>
>
> 5.0 -epsilonRF 78.5<br>>
>
> -------------------------------------<br>>
>
><br>>
>
> In other words, concatenating 11 and 111<br>> gives me<br>>
>
1.xvg, but not with<br>>
>
> 22 and 222......<br>>
>
> How does Gromacs calculate <Mu>^2 and<br>> <Mu^2>......<br>>
>
Mu = Sum q R<br>>
>
where Mu and R are vectors.<br>> ><br>>
>
Obviously if you compare two single<br>> coordinate files<br>>
>
the results will be<br>>
>
different.<br>> ><br>>
>
> Thanks in advance,<br>>
>
> Viswam.<br>>
>
><br>>
>
><br>>
>
><br>>
>
> --<br>>
>
> Viswanadham Sridhara,<br>>
>
> Graduate Research Assistant,<br>>
>
> Old Dominion University, "VIRGINIA".<br>>
>
><br>> _______________________________________________<br>>
>
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>
--<br>>
>
David.<br>> ><br>> ________________________________________________________________________<br>>
>
David van der Spoel, PhD, Assoc. Prof.,<br>> Molecular<br>>
>
Biophysics group,<br>>
>
Dept. of Cell and Molecular Biology, Uppsala<br>>
>
University.<br>>
>
Husargatan 3, Box
596, 75124<br>> Uppsala, Sweden<br>>
>
phone: 46 18 471
4205 fax: 46
18<br>> 511 755<br>>
>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a><br>>
>
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>
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>
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<a href="mailto:request@gromacs.org">request@gromacs.org</a>.<br>> ><br>> ><br>> ><br>> > --<br>> > Viswanadham Sridhara,<br>>
> Graduate Research
Assistant,<br>>
> Old Dominion
University, "VIRGINIA".<br>> ><br>> ><br>> ><br>> ><br>> > --<br>> > Viswanadham Sridhara,<br>> > Graduate Research Assistant,
<br>> > Old Dominion University, "VIRGINIA".<br>> > _______________________________________________<br>> > gmx-users mailing list<br>> > <a href="mailto:gmx-users@gromacs.org">
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<br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics<br>> group,<br>> Dept. of Cell and Molecular Biology, Uppsala University.<br>>
Husargatan 3, Box
596, 75124
Uppsala, Sweden<br>>
phone: 46 18 471
4205 fax: 46
18 511 755<br>> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a><br>> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel
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<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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Old Dominion University, "VIRGINIA".<br>