<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 28/04/2012 3:33 AM, Ho, Tuan A. wrote:
<blockquote
cite="mid:30B5FB5155F14B48BEE5D4206D57EA935B5E429B@it-lightning.sooner.net.ou.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 12 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Times New Roman","serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif"">Dear Gromacs users,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif"">I would like to simulate a
thin film of SWM4_DP water on graphite surface. First, I
equilibrate the water only (run very well), then I add a
graphite surface on it. I freeze the graphite surface but
the graphite surface acted crazily after a few time step
(graphite surface deform critically, “blow”). The error is
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Step
140:<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">The
charge group starting at atom 266 moved than the distance
allowed by the domain decomposition (1.000000) in direction
Z<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">distance
out of cell 1.038218<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Old
coordinates: 0.123 2.627 6.000<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">New
coordinates: 0.013 0.671 11.038<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Old
cell boundaries in direction Z: 5.978 10.000<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">New
cell boundaries in direction Z: 5.660 10.000<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">-------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Program
mdrun, VERSION 4.0.7<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Source
code file: domdec.c, line: 3654<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">Fatal
error:<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:9.0pt;font-family:"Courier New"">A
charge group moved too far between two domain decomposition
steps<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"Courier New"">This
usually means that your system is not well equilibrated<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif"">I don’t understand why I
freeze the graphite surface but the carbon atom moved
around. If it is because of bad contact, I think the water
should be blown instead of carbon atom<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family: "Times New
Roman","serif";">I ran the SPC/E water model
on graphite very well.
</span></p>
</div>
</blockquote>
<br>
Probably you didn't use freezedim on the SOL degrees of freedom when
you used that water model, as you have here.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:30B5FB5155F14B48BEE5D4206D57EA935B5E429B@it-lightning.sooner.net.ou.edu"
type="cite">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif""><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif"">I attached the mdp file, the
topology file.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif"">Please let me know if I did
anything wrong.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif"">Thanks in advance.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif"">Tuan.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif""><o:p> </o:p></span></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>