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<DIV><FONT face=Arial size=2>Hi,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>the bad bond appear in the topology (.top) file.
</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV>veduardo.<BR><BR> Lab. de Fisicoquímica
Molecular<BR> <BR>Facultas de Ciencias<BR> <BR>Universidad de
Chile</DIV></DIV>
<DIV style="FONT: 10pt Tahoma">
<DIV><BR></DIV>
<DIV style="BACKGROUND: #f5f5f5">
<DIV style="font-color: black"><B>From:</B> <A title=nicegromacs@live.cl
href="mailto:nicegromacs@live.cl">nicegromacs</A> </DIV>
<DIV><B>Sent:</B> Wednesday, August 12, 2009 8:28 PM</DIV>
<DIV><B>To:</B> <A
title="mailto:gmx-users@gromacs.org CTRL + clic para seguir el vínculo"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV><B>Subject:</B> [gmx-users] bad bond in polymer</DIV></DIV></DIV>
<DIV><BR></DIV>
<DIV><FONT face=Arial size=2><SPAN class=Apple-style-span
style="WORD-SPACING: 0px; FONT: medium 'Times New Roman'; TEXT-TRANSFORM: none; COLOR: rgb(0,0,0); TEXT-INDENT: 0px; WHITE-SPACE: normal; LETTER-SPACING: normal; BORDER-COLLAPSE: separate; orphans: 2; widows: 2; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px"><SPAN
class=Apple-style-span
style="-webkit-border-horizontal-spacing: 4px; -webkit-border-vertical-spacing: 4px"><SPAN
class=Apple-converted-space><FONT face="Arial Narrow" size=3><SPAN
class=apple-style-span><SPAN lang=EN-US
style="COLOR: black; FONT-FAMILY: 'Courier New'; mso-ansi-language: EN-US"><SPAN
lang=EN-US
style="FONT-SIZE: 12pt; LINE-HEIGHT: 115%; mso-ansi-language: EN-US"><o:p><FONT
face=Calibri>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><SPAN
lang=EN-US
style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'Times New Roman','serif'; mso-ansi-language: EN-US; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: ES-CL">Hi
gmx-users,<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><SPAN
lang=EN-US
style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'Times New Roman','serif'; mso-ansi-language: EN-US; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: ES-CL">I
am building a polymer and I've added the monomer unit to the .rtp file. The
final structure appears with an undesired bond between the monomer units at the
extremes of the polymer. <BR>How can I prevent the monomers at the end forming
the bond?<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><SPAN
lang=EN-US
style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'Times New Roman','serif'; mso-ansi-language: EN-US; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: ES-CL">I
have read other post like <A
href="http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html">http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html</A><SPAN
style="mso-spacerun: yes"> </SPAN>but<SPAN
style="mso-spacerun: yes"> </SPAN>can not avoid this problem .
<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><SPAN
lang=EN-US
style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'Times New Roman','serif'; mso-ansi-language: EN-US; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: ES-CL">Thank
you in advance<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><SPAN
lang=EN-US
style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'Times New Roman','serif'; mso-ansi-language: EN-US; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: ES-CL">veduardo.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><SPAN
style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'Times New Roman','serif'; mso-ansi-language: ES-CL; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: ES-CL">Lab.
de Fisicoquímica Molecular<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><SPAN
style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'Times New Roman','serif'; mso-ansi-language: ES-CL; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: ES-CL">Facultas
de Ciencias</SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><SPAN
lang=EN-US
style="FONT-SIZE: 12pt; COLOR: black; FONT-FAMILY: 'Times New Roman','serif'; mso-ansi-language: EN-US; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: ES-CL">Universidad
de Chile<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt; LINE-HEIGHT: normal"><FONT
face=Arial size=2></FONT></FONT></o:p></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 10pt"><FONT face=Arial
size=2></FONT></SPAN></SPAN></FONT> </P></SPAN></SPAN></SPAN></FONT></DIV>
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