<HTML>
<font style="font-size: 10pt;"><div><meta http-equiv="Content-Type"
content="text/html; charset=us-ascii"><meta name="ProgId"
content="Word.Document"><meta name="Generator" content="Microsoft Word 11">
<meta name="Originator" content="Microsoft Word 11"><link rel="File-List"
href="file:///C:%5CDOCUME%7E1%5Camin%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml">
<!--[if gte mso 9]><xml>
<w:WordDocument>
<w:View>Normal</w:View>
<w:Zoom>0</w:Zoom>
<w:PunctuationKerning/>
<w:ValidateAgainstSchemas/>
<w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid>
<w:IgnoreMixedContent>false</w:IgnoreMixedContent>
<w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText>
<w:Compatibility>
<w:BreakWrappedTables/>
<w:SnapToGridInCell/>
<w:WrapTextWithPunct/>
<w:UseAsianBreakRules/>
<w:DontGrowAutofit/>
</w:Compatibility>
<w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel>
</w:WordDocument>
</xml><![endif]--><!--[if gte mso 9]><xml>
<w:LatentStyles DefLockedState="false" LatentStyleCount="156">
</w:LatentStyles>
</xml><![endif]--><style>
<!--
/* Font Definitions */
@font-face
{font-family:Mangal;
panose-1:0 0 4 0 0 0 0 0 0 0;
mso-font-charset:1;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:32768 0 0 0 0 0;}
@font-face
{font-family:"DejaVu Sans";
mso-font-charset:128;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 0 0 0 0;}
@font-face
{font-family:"\@DejaVu Sans";
mso-font-charset:128;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-parent:"";
margin:0in;
margin-bottom:.0001pt;
mso-pagination:none;
mso-hyphenate:none;
font-size:12.0pt;
font-family:"Times New Roman";
mso-fareast-font-family:"DejaVu Sans";
mso-bidi-font-family:Mangal;
mso-font-kerning:.5pt;
mso-ansi-language:EN-GB;
mso-fareast-language:HI;
mso-bidi-language:HI;}
@page Section1
{size:8.5in 11.0in;
margin:56.7pt 56.7pt 56.7pt 56.7pt;
mso-header-margin:.5in;
mso-footer-margin:.5in;
mso-paper-source:0;}
div.Section1
{page:Section1;}
-->
</style><!--[if gte mso 10]>
<style>
/* Style Definitions */
table.MsoNormalTable
{mso-style-name:"Table Normal";
mso-tstyle-rowband-size:0;
mso-tstyle-colband-size:0;
mso-style-noshow:yes;
mso-style-parent:"";
mso-padding-alt:0in 5.4pt 0in 5.4pt;
mso-para-margin:0in;
mso-para-margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:"Times New Roman";
mso-ansi-language:#0400;
mso-fareast-language:#0400;
mso-bidi-language:#0400;}
</style>
<![endif]-->
<p class="MsoNormal"><span lang="EN-GB">Dear users GROMACS</span></div>
<p class="MsoNormal"></div>
<p class="MsoNormal"><span lang="EN-GB">I have a problem using GROMACS</span>
</div>
<p class="MsoNormal"></div>
<p class="MsoNormal"><span lang="EN-GB">When the program runs by
"pdb2gmx" Option, the file X.top doesnot any information about force
constant X.pdb file and I enter informations handling in this file.</span>
</div>
<p class="MsoNormal"></div>
<p class="MsoNormal"><span lang="EN-GB">Where the problem comes from??</span>
</div>
<p class="MsoNormal"><a name="result_box"></a><span lang="EN-GB">In
addition,<a name="result_box1"></a>How can I make in Gromacs<span style="">
</span>a regular cluster structure of a molecule ?</span></div>
<p class="MsoNormal"><a name="result_box2"></a><span lang="EN-GB">Whether by
g_cluster option? <a name="result_box3"></a>If this option could be to do
this,
please help me to make a cluster structure from a adamantine molecule in a
box
in sizes: x=10, y=10, z=10 an put 125 number from adamantane mulecule( in
each
direction 5 molecule means 5*5*5<span style=""> </span>and
distance every molecule of each other will be 1 nm) in this box.</span></div>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></div>
<p class="MsoNormal"><span lang="EN-GB">Thanks alot</span></div>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></div>
</div></font>
Jafar Azamat <br><br>Molecular Simulations Lab.<br>Faculty of
Basic Sciences<br>Azerbaijan University of Tarbiat Moallem.<br>
</HTML>