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On 14/10/2011 12:38 AM, liaoxyi wrote:
<blockquote
cite="mid:526cc754.77a4.132fd815ec4.Coremail.liaoxyi@163.com"
type="cite">
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<div><span style="FONT-FAMILY: 'Courier New'; FONT-SIZE: 9pt;
mso-fareast-font-family: 宋体; mso-ansi-language: ZH-CN;
mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman"><font size="3">Dear
all, <o:p></o:p></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman"><font size="3">Thank
you for giving me some hints for my problems.</font></font></span><span
lang="EN-US"></span></p>
<o:p></o:p></span>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font face="Times New Roman"><font size="3">The
problems has been solved now, the key is <o:p></o:p></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font
size="3"><span lang="EN-US"><font face="Times New Roman">to
adjust the gb_dielectric_offset to a smaller value
like 0.05</font></span><span style="FONT-FAMILY: 宋体;
mso-ascii-font-family: 'Times New Roman';
mso-hansi-font-family: 'Times New Roman'">，</span></font></p>
<p style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New Roman">then
the <i>minimization </i><span style="">gets going
normally. </span></font></font></span></p>
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</blockquote>
<br>
You should use the value recommended for the model you are
implementing - the default is suitable for the models in GROMACS.<br>
<br>
<blockquote
cite="mid:526cc754.77a4.132fd815ec4.Coremail.liaoxyi@163.com"
type="cite">
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14px; font-family: arial;">
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<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
lang="EN-US"><font size="3"><font face="Times New Roman"><span
style="mso-bidi-font-style: italic"><o:p></o:p></span></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
style="mso-bidi-font-style: italic" lang="EN-US"><font
size="3"><font face="Times New Roman">Subsequently, the
NVT goes well.<o:p></o:p></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span
style="mso-bidi-font-style: italic" lang="EN-US"><font
size="3"><font face="Times New Roman">Still, I don’t
quite understand what role <o:p></o:p></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font
size="3"><font face="Times New Roman"><span
style="mso-bidi-font-style: italic" lang="EN-US">the </span><span
lang="EN-US">gb_dielectric_offset <span
style="mso-bidi-font-style: italic">actually</span>
plays ?</span></font></font></p>
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</blockquote>
<br>
You will need to read some literature here - and should have done
before changing the default values :-). I suggest starting with the
OBC paper referenced in the manual.<br>
<br>
Mark<br>
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