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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear David, <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 already did that, and my impression is that it is still broken.<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 have a liquid that includes the ions PF6- <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Obviously P is for all purposes at the center of mass of the
molecules.<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 I compute the velocity autocorrelation function for P I
get a function<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>that</span></font></span><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> is totally
different from the one I get for PF6-<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 know the correlation function for P is right because I computed
it separately.<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'>Thanks for looking into this.<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'>>> Hi, I’m trying to use <span class=SpellE>g_velacc</span>
to compute the velocity autocorrelation<o:p></o:p></span></font></p>
<p class=MsoNormal><span class=GramE><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>>> function for a set of
molecules.</span></font></span><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'>>> When I compute <span class=SpellE>g_velacc</span>
for atoms it gives the correct answer (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'>>> my own program to check)<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'>>> When I compute it for molecules (with option
–mol and <span class=SpellE>and</span> index file<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>>> with molecules not atoms)<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 get strange 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'>>><span style='mso-spacerun:yes'> </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'>>> <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 looked at the source code (<span class=SpellE>admitedly</span>
I’m a much better <span class=SpellE><span class=GramE>fortran</span></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'>>> <span class=GramE>programmer</span> than c) but
these few lines look weird to me.<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'>>> Can anybody tell me <span class=GramE>if<span
style='mso-spacerun:yes'> </span>line</span> 7 to 9 they are right or
not?<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'>--please replace by YY and ZZ and test. Could you report
back whether that<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>--solves the problem? I'm afraid this program is not very
often used, and<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>--hence not well tested.<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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