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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi <span class=SpellE><span class=GramE>david</span></span>,<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I have a couple questions about <span
class=SpellE>g_hbond</span>. I noticed an Oct <span class=GramE>2003 <span
style='mso-spacerun:yes'>&nbsp;</span>post</span> where you mention completely
rewriting <span class=SpellE>g_hbond</span>.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Is the second column in the &#8211;ac output
a fit to the first column? <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Also I noticed that when I use &#8211;<span
class=SpellE>noda</span> and reduce the &#8211;<span class=GramE>r <span
style='mso-spacerun:yes'>&nbsp;</span>value</span> to .25 <span
style='mso-spacerun:yes'>&nbsp;</span>it doesn&#8217;t work. <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>It gives me the same output as if I didn&#8217;t
use the &#8211;<span class=SpellE>noda</span> option. I then compared my
results using g_hbond_3.1.4 (r .25) and <span class=SpellE>g_hbond</span> (r .35)
and got <o:p></o:p></span></font></p>

<p class=MsoNormal><span class=GramE><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>very</span></font></span><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> different results. The version 3.2 <span class=GramE>C(</span>t)
decays slower. My system is a solute <span class=GramE>in<span
style='mso-spacerun:yes'>&nbsp; </span>a</span> box of solvent molecules. Since
I can&#8217;t use the &#8211;<span class=SpellE>noda</span> option I can&#8217;t
make a direct <o:p></o:p></span></font></p>

<p class=MsoNormal><span class=GramE><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>comparison</span></font></span><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>. Any help would be greatly appreciated.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Ilya<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in;mso-list:l0 level3 lfo1;
tab-stops:list .5in'><![if !supportLists]><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;mso-fareast-font-family:Arial;
color:navy'><span style='mso-list:Ignore'>3.1.4<font size=1
face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></font></span></span></font><![endif]><span class=SpellE><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>g_hbond</span></font></span><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'> &#8211;r .25 &#8211;shell
1.0 -ac<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>3.2<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
class=SpellE>g_<span class=GramE>hbond</span></span><span class=GramE><span
style='mso-spacerun:yes'>&nbsp; </span>-</span>r.35<span
style='mso-spacerun:yes'>&nbsp; </span>-shell 1.0 -ac<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoPlainText style='margin-left:1.5in'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>

<p class=MsoPlainText style='margin-left:1.5in'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><span
style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><o:p></o:p></span></font></p>

<p class=MsoPlainText style='margin-left:2.0in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>----------------------------------------------------------------------------------------------<o:p></o:p></span></font></p>

<p class=MsoPlainText style='margin-left:2.0in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Dr. Ilya Chorny<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><span style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;</span>Department of
Pharmaceutical Chemistry<o:p></o:p></span></font></p>

<p class=MsoPlainText style='margin-left:2.0in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>DOE/SLOAN Postdoctoral Researcher<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></font><st1:place><st1:PlaceType>University</st1:PlaceType>
 of <st1:PlaceName>California</st1:PlaceName></st1:place>, <st1:City><st1:place>San
  Francisco</st1:place></st1:City><o:p></o:p></p>

<p class=MsoPlainText style='margin-left:2.0in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Tel:<span style='mso-spacerun:yes'>&nbsp;
</span>(415)-476-6875<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>600 16th st<o:p></o:p></span></font></p>

<p class=MsoPlainText style='margin-left:2.0in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Fax:<span style='mso-spacerun:yes'>&nbsp;
</span>(415)502-4222<span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></font><st1:place><st1:City>San Francisco</st1:City>, <st1:State>CA</st1:State>
 <st1:PostalCode>94107</st1:PostalCode></st1:place><o:p></o:p></p>

<p class=MsoPlainText style='margin-left:2.0in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Cell: (408)887-8496<o:p></o:p></span></font></p>

<p class=MsoPlainText style='margin-left:2.0in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'><span
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>Email: ichorny@maxwell.ucsf.edu<o:p></o:p></span></font></p>

<p class=MsoPlainText style='margin-left:2.0in'><font size=2 face="Courier New"><span
style='font-size:10.0pt'>----------------------------------------------------------------------------------------------<o:p></o:p></span></font></p>

<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p>&nbsp;</o:p></span></font></p>

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