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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3>Hello,<?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"><FONT size=3><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><SPAN
style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>I want to find a best (or stable)
conformation for one molecular in water. </SPAN></FONT></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"><FONT size=3><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'">First, I
built many conformation</SPAN><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-fareast-font-family: 新細明體; mso-bidi-font-family: 'Arial Unicode MS'">s</SPAN><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"> for my
molecular. Then, I run MD to get</SPAN></FONT></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"><FONT size=3><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-font-kerning: 0pt; mso-bidi-font-family: 'Arial Unicode MS'">local
minima</SPAN><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'">. I want
to know <SPAN style="mso-bidi-font-style: italic">the free energy difference
</SPAN>for all conformation</SPAN></FONT></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"><FONT size=3><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'">in
molecular. If one conformation had lowest free energy <SPAN
style="mso-bidi-font-style: italic">difference</SPAN>, I think
</SPAN></FONT></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"><FONT size=3><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'">it is
better than other</SPAN><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-fareast-font-family: 新細明體; mso-bidi-font-family: 'Arial Unicode MS'">s</SPAN><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'">.</SPAN><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-font-kerning: 0pt; mso-bidi-font-family: 'Arial Unicode MS'"><o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal
style="MARGIN: 0cm -7.7pt 0pt 0cm; mso-para-margin-right: -.64gd"><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3><SPAN style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>Now I want to know <SPAN
style="mso-bidi-font-style: italic">the free energy difference </SPAN>between
conformation N and </FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm -7.7pt 0pt 0cm; mso-para-margin-right: -.64gd"><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3>conformation A.</FONT></SPAN><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3>(N = A, B, C …, etc). Compare the results.<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3><SPAN style="mso-spacerun: yes"> </SPAN>I don’t know how to do this
work.<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><o:p><FONT
size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3>Thanks in advance for your help,<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-fareast-font-family: 新細明體; mso-bidi-font-family: 'Arial Unicode MS'"><o:p><FONT
size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><o:p><FONT
size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3></FONT></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3></FONT></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3>MLYu <o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><?xml:namespace
prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:place
w:st="on"><st1:PlaceName w:st="on"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'">Nation</SPAN></st1:PlaceName><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'">
<st1:PlaceName w:st="on">Taiwan</st1:PlaceName> <st1:PlaceType
w:st="on">University , Chemistry </st1:PlaceType></SPAN></st1:place><SPAN
lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><A
href="mailto:mlyu@rs350.ch.ntu.edu.tw"><FONT
size=3>mlyu@rs350.ch.ntu.edu.tw</FONT></A><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: Batang; mso-bidi-font-family: 'Arial Unicode MS'"><FONT
size=3>tel :
886-2-33661168<o:p></o:p></FONT></SPAN></P></FONT></DIV></BODY></HTML>