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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Sorry if this appears posted more than once<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>This is the third time I send it and it seems like it is not
getting posted.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>C.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>-----------------------------------------------------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear David, I did try changing the code as you suggested.
But it gave the wrong results. Let me explain,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I wrote a bunch <span class=GramE>of<span
style='mso-spacerun:yes'> </span>programs</span> to take trajectories in .<span
class=SpellE>gro</span> format (which I obtained by <span class=SpellE>trjconv</span>
–<span class=SpellE>nojump</span> - … from the original <span
class=SpellE>trr</span> ). For each of the PF6- molecules in the box I computed
the trajectory of the center of mass and proceeded to compute the averaged time
correlation function of it with another little program I wrote.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I compared this result to<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>1) <span class=GramE>unchanged</span> <span class=SpellE>g_velacc</span><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>2) <span class=GramE>changing</span> XX <span class=SpellE>XX</span>
for YY ZZ<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>3) <span class=GramE>changing</span> XX <span class=SpellE>XX</span>
for YY ZZ and modifying the loop as you suggested.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>My pedestrian computation gives exactly the same result as
in 2, 1 is a little different, and 3 is totally different.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>This is my understanding of the reason why the cm <span
class=SpellE>vac</span> and the p <span class=SpellE>vac</span> are so widely
different:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>The reason why the velocity autocorrelation function for P
and for the center of mass are way different is that there is a lot of very
high frequency movement of P about the CM.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>If one computes the trajectory of one particular P and
compares it to that of the center of mass of its corresponding PF6- ion, one
obtains basically identical trajectories (as one would expect). The only
difference is very high frequency (but low intensity) oscillations in the case
of P. Therefore trajectories look nearly identical but velocities are widely
different due to the constant change of direction of velocity of P.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Anyway this is what I have so far, I felt that those VAC
should have been similar, but really CM and P only should share the low
frequency part, P is in average at the CM but it’s fluctuating like crazy
around it and the <span class=SpellE>vac</span> displays these high frequency
oscillations.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Therefore what you are saying in your last posting puzzles
me. Are you really sure?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I did write my own code to check the results …<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thanks!!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Claudio.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>-----------------------------------------------------------------------------------------</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Claudio J. Margulis</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Assistant Professor</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Department of Chemistry</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><st1:place><st1:PlaceType><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>University</span></font></st1:PlaceType><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial;mso-no-proof:
yes'> of </span></font><st1:PlaceName><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>Iowa</span></font></st1:PlaceName></st1:place><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>319 CB</span></font><span style='mso-no-proof:
yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>319-335-0615 (office)</span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><a
href="http://www.uiowa.edu/~chemdept/faculty/margulis/index.html">http://www.uiowa.edu/~chemdept/faculty/margulis/index.html</a></span></font><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>-----------------------------------------------------------------------------------------</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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