Hello again,<br>
Thanks David for the quick response, but i have few doubts with the output files of g_dipoles.....<br>
I am just pasting files, so that it will be easy for everyone to understand.....but only a part of the files though,<br>
------<br>
# This file was created by g_dipoles_AMD32<br>
# which is part of G R O M A C S:<br>
# GROningen MAchine for Chemical Simulation<br>
# All this happened at: Wed Nov 9 13:49:28 2005<br>
#<br>
@ title "Total dipole moment of the simulation box vs. time"<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "Total Dipole Moment (Debye)"<br>
@TYPE xy<br>
@ view 0.15, 0.15, 0.75, 0.85<br>
@ legend on<br>
@ legend box on<br>
@ legend loctype view<br>
@ legend 0.78, 0.8<br>
@ legend length 2<br>
@ s0 legend "M\sx \N"<br>
@ s1 legend "M\sy \N"<br>
@ s2 legend "M\sz \N"<br>
@ s3 legend "|M\stot \N|"<br>
0 2.64626166e+02 1.16440350e+03 -8.75332770e+01 1.19729888e+03<br>
4 9.62820668e+02 1.12993143e+03 -2.29642353e+02 1.50216653e+03<br>
8 1.04575875e+03 6.88685425e+02 -2.78564322e+02 1.28276929e+03<br>
<br>
<br>
------<br>
# This file was created by g_dipoles_AMD32<br>
# which is part of G R O M A C S:<br>
# Gromacs Runs One Microsecond At Cannonball Speeds<br>
# All this happened at: Wed Nov 9 13:52:51 2005<br>
#<br>
@ title "Total dipole moment"<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "D"<br>
@TYPE xy<br>
@ view 0.15, 0.15, 0.75, 0.85<br>
@ legend on<br>
@ legend box on<br>
@ legend loctype view<br>
@ legend 0.78, 0.8<br>
@ legend length 2<br>
@ s0 legend "< |M|\S2\N >"<br>
@ s1 legend "< |M| >\S2\N"<br>
@ s2 legend "< |M|\S2\N > - < |M| >\S2\N"<br>
@ s3 legend "< |M| >\S2\N / < |M|\S2\N >"<br>
0 1.434e+06 1.434e+06 1.921e-11 1.000e+00<br>
4 1.845e+06 1.718e+06 1.272e+05 9.310e-01<br>
8 1.779e+06 1.602e+06 1.762e+05 9.009e-01<br>
------<br><br>
<br>
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.<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 both < |M|\S2\N > and < |M| >\S2\N", so that their
ratio is 1, 4th column in second file........<br>
But how are they calculated for t =4 ...and so on.....<br>
<br>
--------------------<br>
<br>
I hope I am clear this time....<br>
Thanks in advance<br>
<br>
Viswam..<br>
<br>
<br>
<br>
<br>
<div><span class="gmail_quote">On 11/9/05, <b class="gmail_sendername">Viswanadham Sridhara</b> <<a href="mailto:muta.mestri@gmail.com">muta.mestri@gmail.com</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;">
Hello David,<br>
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)...<br>
Thanks,<div><span class="e" id="q_10776a5207465f4b_1"><br>
<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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">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 14:38 -0500, Viswanadham 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 dipole moment, --
<br>> >full.xvg (This is with option -o)<br>> b)then i divided the whole trajectory into two parts and tried to find<br>> the dipole moment, first half-->fh.xvg and second half sh.xvg.<br>> Obviously fh.xvg
and sh.xvg combined is equal to full.xvg.<br>><br>> But, when i use option -a in g_dipoles, and tried to find <Mu>^2 -<br>> <Mu^2> for the whole trajectory, the n umbers I 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 2.273 -mumax 5.0 -<br>> epsilonRF 78.5<br>> g_dipoles -f firsthalf.gro -s dppc.tpr -o 11 -a 22 -mu 2.273 -mumax<br>> 5.0
-epsilonRF 78.5<br>> g_dipoles -f secondhalf.gro -s dppc.tpr -o 111 -a 222 -mu 2.273 -mumax<br>> 5.0 -epsilonRF 78.5<br>> -------------------------------------<br>><br>> In other words, concatenating 11 and 111 gives me
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 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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</a>.<br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
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<br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>
Old Dominion University, "VIRGINIA".<br>
</span></div></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>Old Dominion University, "VIRGINIA".<br>