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style="FONT-SIZE: 12pt; FONT-FAMILY: 幼圆; mso-hansi-font-family: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt">Tsjerk
Wassenaar, thank you very much for you suggestion even if most of them have been
manipulated.</SPAN><SPAN lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt; mso-ascii-font-family: 幼圆; mso-fareast-font-family: 幼圆"> </SPAN><SPAN
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<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt"> <o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><I><SPAN lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt">"Write
out the energies at every step and check which of the energy<BR>contributions
goes astray. This may give you a good clue to where<BR>you're mistake is. Also,
run through the topology again, by hand,<BR>checking all bonds, angles,
dihedrals, exclusion (implicit ones!),<BR>etc."</SPAN></I><SPAN lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt"><o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 12pt; COLOR: green; FONT-FAMILY: 幼圆; mso-hansi-font-family: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt">when
the explosion happened, the energy of bond, angle and potential will were
increase. And the topology has been checked several times. </SPAN><SPAN
lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt"><o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt"> <o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt"> <o:p></o:p></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 幼圆; mso-hansi-font-family: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt">Now
I</SPAN><SPAN lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt; mso-ascii-font-family: 幼圆; mso-fareast-font-family: 幼圆"> </SPAN><SPAN
lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 幼圆; mso-hansi-font-family: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt">increase
the cutoff of VDW & Coulomb from 0.9 to 1.5. The system</SPAN><SPAN
lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt; mso-ascii-font-family: 幼圆; mso-fareast-font-family: 幼圆"> </SPAN><SPAN
lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 幼圆; mso-hansi-font-family: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt">looks
ok from last night to this time. If the problem is fixed, I conclude that cutoff
0.9</SPAN><SPAN lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt; mso-ascii-font-family: 幼圆; mso-fareast-font-family: 幼圆"> </SPAN><SPAN
lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 幼圆; mso-hansi-font-family: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt">is
not enough for electric system.</SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 幼圆; mso-hansi-font-family: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt"></SPAN> </P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: left; mso-pagination: widow-orphan"
align=left><SPAN lang=EN-US
style="FONT-SIZE: 24pt; COLOR: green; FONT-FAMILY: 幼圆; mso-hansi-font-family: 宋体; mso-bidi-font-family: 宋体; mso-font-kerning: 0pt"><FONT
face=宋体 color=#000000 size=3>Hope this conclusion is helpful for GMX
users.</FONT></SPAN></P></FONT></DIV>
<DIV><FONT face=幼圆 size=6></FONT> </DIV>
<DIV><FONT face=幼圆></FONT> </DIV>
<DIV><FONT face=幼圆></FONT> </DIV>
<DIV><EM>Message: 2<BR>Date: Wed, 7 Mar 2007 17:49:30 +0100<BR>From: "Tsjerk
Wassenaar" <</EM><A
href="mailto:tsjerkw@gmail.com"><EM>tsjerkw@gmail.com</EM></A><EM>><BR>Subject:
Re: Re: [gmx-users] vacuum right but melt collapse<BR>To: "kitty ji" <</EM><A
href="mailto:jiqing@iccas.ac.cn"><EM>jiqing@iccas.ac.cn</EM></A><EM>>,
"Discussion list for GROMACS<BR>users" <</EM><A
href="mailto:gmx-users@gromacs.org"><EM>gmx-users@gromacs.org</EM></A><EM>><BR>Message-ID:<BR><</EM><A
href="mailto:8ff898150703070849r59cb8a8dr60b894a881fcc331@mail.gmail.com"><EM>8ff898150703070849r59cb8a8dr60b894a881fcc331@mail.gmail.com</EM></A><EM>><BR>Content-Type:
text/plain; charset=GB2312; format=flowed<BR><BR>Hi Ji Qing,<BR><BR>Write out
the energies at every step and check which of the energy<BR>contributions goes
astray. This may give you a good clue to where<BR>you're mistake is. Also, run
through the topology again, by hand,<BR>checking all bonds, angles, dihedrals,
exclusion (implicit ones!),<BR>etc.<BR><BR>Good luck,<BR><BR>Tsjerk<BR><BR>On
3/7/07, kitty ji <</EM><A
href="mailto:jiqing@iccas.ac.cn"><EM>jiqing@iccas.ac.cn</EM></A><EM>>
wrote:<BR>><BR>><BR>> Thanks Mark.<BR>> But when one polymer chain
was used, non-bonded interaction has already been<BR>> there. Because one
chain means C44H156O22.<BR>> After all, I'd like to try more
chains.<BR>><BR>> Message: 1<BR>> Date: Tue, 06 Mar 2007 17:01:52
+1100<BR>> From: Mark Abraham <</EM><A
href="mailto:Mark.Abraham@anu.edu.au"><EM>Mark.Abraham@anu.edu.au</EM></A><EM>><BR>>
Subject: Re: [gmx-users] vacuum right but melt collapse<BR>> To: Discussion
list for GROMACS users <</EM><A
href="mailto:gmx-users@gromacs.org"><EM>gmx-users@gromacs.org</EM></A><EM>><BR>>
Message-ID: <</EM><A
href="mailto:45ED03D0.6010803@anu.edu.au"><EM>45ED03D0.6010803@anu.edu.au</EM></A><EM>><BR>>
Content-Type: text/plain; charset=GB2312<BR>><BR>> kitty ji wrote:<BR>>
> Hi GMX user:<BR>> ><BR>> > A model for Poly(vinyl methyl ether)
was built with OPLS force field (<BR>> > all H ).<BR>> ><BR>>
><BR>> ><BR>> > When the model was run alone (a single chain) in
vacuum, anything goes ok.<BR>> ><BR>> ><BR>> ><BR>> >
But with 45 chains box, the system will be collapse with a little bond<BR>>
> elongates abnormal whatever in NVT or NPT.<BR>> ><BR>>
><BR>> ><BR>> > The relax time of pressure and temperature were
adjust but no helpful.<BR>> ><BR>> ><BR>> ><BR>> > How
can I found some possible reason and then fix it ? Any advise will<BR>> >
be appreciated.<BR>><BR>> If an isolated molecule doesn't do anything
strange, and two more more<BR>> do, then you have a problem with
inter-molecular interactions, i.e. the<BR>> non-bonded ones. Try with just 2
chains to verify this... and look<BR>> carefully at the atom types and the
non-bonded parameters for them.<BR>><BR>>
Mark<BR>><BR>><BR>><BR>>
*************************************************<BR>> Ji Qing<BR>>
Institute of Chemistry, Chinese Academy of Sciences<BR>> Tel:
0086-10-62562894 £¬82618423<BR>>
*************************************************<BR>>
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<BR>Tsjerk A. Wassenaar, Ph.D.<BR>Junior UD (post-doc)<BR>Biomolecular NMR,
Bijvoet Center<BR>Utrecht University<BR>Padualaan 8<BR>3584 CH Utrecht<BR>The
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