<html><head><meta http-equiv="content-type" content="text/html; charset=GB2312"><style>body { line-height: 1.5; }blockquote { margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em; }p { margin-top: 0px; margin-bottom: 0px; }div.foxdiv20181220142851701645 { }body { font-size: 10.5pt; font-family: 微软雅黑; color: rgb(0, 0, 0); line-height: 1.5; }</style></head><body>
<div><span></span></div><blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;"><div><div class="FoxDiv20181220142851701645"><blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;"><div><div class="FoxDiv20181220142056113227"><blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;"><div><div class="FoxDiv20181220141903224369"><blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;"><div><div class="FoxDiv20181220141630774603"><blockquote style="margin-top: 0px; margin-bottom: 0px; margin-left: 0.5em;"><div class="FoxDiv20181220140250306629"><div>Dear GROMACS developer,</div><div><br></div><div>I am Youliang Zhu (My homepage: <span style="background-color: rgba(0, 0, 0, 0); font-size: 10.5pt; line-height: 1.5;"></span><a href="http://galamost.ciac.jl.cn/view.php?id=625" style="font-size: 10.5pt; line-height: 1.5; background-color: window;">http://galamost.ciac.jl.cn/view.php?id=625</a><span style="color: rgb(0, 0, 0); font-size: 10.5pt; line-height: 1.5; background-color: rgba(0, 0, 0, 0);"> </span><span style="background-color: window; font-size: 10.5pt; line-height: 1.5;">).</span></div><span style="color: rgb(0, 0, 0); background-color: rgba(0, 0, 0, 0);"></span><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">I met a problem when I try to reproduce the Coulomb interaction with reaction field zero of GROMACS in our codes.</span></div><div>With a same frame of DUPC membrane system, I compared the outputing potential between GROMACS and our codes(the code file is appended).</div><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">I could well reproduce the bond, angle, Lennard Jones </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">with </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">switch function</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">, and Columb interactions with </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">switch function. </span></div><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">However, I could not reproduce the </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">Columb interaction with reaction-field-zero. Please see the details in appended file.</span></div><div>It 's <span style="background-color: rgba(0, 0, 0, 0); font-size: 10.5pt; line-height: 1.5;">weird that I could reproduce the </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">Columb interaction</span><span style="color: rgb(0, 0, 0); font-size: 10.5pt; line-height: 1.5; background-color: rgba(0, 0, 0, 0);"> when</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;"> I let Krf=0 in two codes.</span></div><div><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">I wonder if there is any </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">differences between my code and GROMACS implementations.</span></div><div><br></div><div>I will greatly appriciate any your <span style="background-color: rgba(0, 0, 0, 0); font-size: 10.5pt; line-height: 1.5;">respondence</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">.</span></div>
<div><br></div><div>Best Regards,</div><div>Youliang</div><div><br></div><div><br></div><div><!--[if gte mso 9]><xml>
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<p class="MsoNormal" align="left" style="text-align: justify; margin: 0px 0cm; font-size: 10.5pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:宋体;mso-font-kerning:0pt">I use following script
commands in my mdp file to implement Coulomb interaction with
reaction-field-zero.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin: 0px 0cm; text-align: justify; font-size: 10.5pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;
font-family:"Times New Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin: 0px 0cm; text-align: justify; font-size: 10.5pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;
font-family:"Times New Roman","serif";color:#0070C0">coulombtype = reaction-field <o:p></o:p></span></p>
<p class="MsoNormal" style="margin: 0px 0cm; text-align: justify; font-size: 10.5pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;
font-family:"Times New Roman","serif";color:#0070C0">rcoulomb = 1.2<o:p></o:p></span></p>
<p class="MsoNormal" style="margin: 0px 0cm; text-align: justify; font-size: 10.5pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;
font-family:"Times New Roman","serif";color:#0070C0">epsilon_r = 15 <o:p></o:p></span></p>
<p class="MsoNormal" style="margin: 0px 0cm; text-align: justify; font-size: 10.5pt; font-family: Calibri, sans-serif;"><span lang="EN-US" style="mso-bidi-font-size:10.5pt;
font-family:"Times New Roman","serif";color:#0070C0">epsilon_rf = 0<o:p></o:p></span></p>
<!--EndFragment--></div><div><br></div><div><br></div><div><br></div><div><br></div>
<hr style="width: 210px; height: 1px;" align="left" color="#b5c4df" size="1">
<div><span><div style="MARGIN: 10px; FONT-FAMILY: verdana; FONT-SIZE: 10pt"><div style="font-family: Verdana; font-size: small;"><span style="color: rgb(0, 0, 255); line-height: 1.5; background-color: window;">Dr. You-Liang Zhu (朱有亮)</span></div><div style="font-family: Verdana; font-size: small;"><span style="font-size: 13px; background-color: rgba(0, 0, 0, 0);"><font color="#0000ff">State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, </font></span></div><div style="font-family: Verdana; font-size: small;"><span style="font-size: 13px; background-color: rgba(0, 0, 0, 0);"><font color="#0000ff">Chinese Academy of Sciences, Changchun 130022, China.</font></span></div><div style="font-family: Verdana; font-size: small;"><font color="#0000ff">Email: youliangzhu@ciac.ac.cn</font></div><div style="font-family: Verdana; font-size: small;"><font color="#0000ff">Phone: +86 043185262512(office)</font></div><div style="font-family: Verdana; font-size: small;"><font color="#0000ff">Mobile: +86 15948268485</font></div><div style="font-family: Verdana; font-size: small;"><font color="#0000ff">Fax: +86 <span style="line-height: 1.5; background-color: window;">043185262969</span></font></div></div></span></div>
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