Hi again,<br>
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.......<br>
Hope someone clarifies to me briefly how they are calculated at t =0 and for t = 0 + of the simulation.<br>
Thanks in advance,<br>
Viswam.<br><br><div><span class="gmail_quote">On 11/9/05, <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 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 assumed to be<br>> equal in the very first time step, but from 4ps in th is 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 equal for<br>> both < |M|\S2\N > and < |M| >\S2\N", so that their ratio is 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 converts e<br>nm to Debye).<br><br>void mol_dip(int k0,int k1,atom_id ma[],rvec x[],t_atom atom[],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>> wrote:<br>> Hello David,<br>> Then why are the files 11.xvg and 111.xvg same as first half<br>> of 1.xvg and the second half of 1.xvg respectively, in other<br>
> words the total dipole moment of the frames for the whole<br>> trajectory is same as when calculated separately for the first<br>> and second halves and concatenated, but not the dipole plus
<br>> fluctuations...........(22.xvg and 222.xvg are 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, Viswanadham<br>> Sridhara wrote:<br>> > Hello Everyone,<br>>
> Can anyone explain me how g_dipoles exactly work?<br>>
> I am just briefly explaining what I did.<br>>
> a) I took the whole trajectory and tried to find<br>> dipole moment, --<br>>
> >full.xvg (This is with option -o)<br>>
> b)then i divided the whole trajectory into two parts<br>> and tried to find<br>>
> the dipole moment, first half-->fh.xvg and second<br>> half sh.xvg.<br>>
> Obviously fh.xvg and sh.xvg combined is equal to<br>> full.xvg.<br>> ><br>>
> But, when i use option -a in g_dipoles, and tried to<br>> find <Mu>^2 -<br>>
> <Mu^2> for the whole trajectory, the n umbers I<br>> found are different<br>>
> for the trajectory when divided into two parts.<br>> ><br>> > -------------------<br>>
> g_dipoles -f full.gro -s dppc.tpr -o 1 -a 2 -mu<br>> 2.273 -mumax 5.0 -<br>> > epsilonRF 78.5<br>>
> g_dipoles -f firsthalf.gro -s dppc.tpr -o 11 -a 22 -<br>> mu 2.273 -mumax<br>> > 5.0 -epsilonRF 78.5<br>>
> g_dipoles -f secondhalf.gro -s dppc.tpr -o 111 -a<br>> 222 -mu 2.273 -mumax<br>> > 5.0 -epsilonRF 78.5<br>>
> -------------------------------------<br>> ><br>>
> In other words, concatenating 11 and 111 gives me<br>> 1.xvg, but not with<br>> > 22 and 222......<br>>
> How does Gromacs calculate <Mu>^2 and <Mu^2>......<br>> Mu = Sum q R<br>> where Mu and R are vectors.<br>><br>>
Obviously if you compare two single 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>>
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________________________________________________________________________<br>>
David van der Spoel, PhD, Assoc. Prof., Molecular<br>> Biophysics group,<br>>
Dept. of Cell and Molecular Biology, Uppsala<br>> 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>>
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<br>> Old Dominion University, "VIRGINIA".<br>><br>><br>><br>><br>> --<br>> Viswanadham Sridhara,<br>> Graduate Research Assistant,<br>> Old Dominion University, "VIRGINIA".
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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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<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>
Old Dominion University, "VIRGINIA".<br>