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<div>Hi </div>
<div>My simulation broke down and the simulation procedues are as follows.</div>
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<div>1. center a protein molecule in the simulation box</div>
<div>2. put 20 ligands around the protein with  &quot; genbox &quot; command</div>
<div>3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software.</div>
<div>4. solvent addition , with the command &quot; genbox <strong><font face="Courier New">-vdwd</font></strong>  0.2   &quot; </div>
<div>5. Addition of ions, with the command &quot; <span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">genion &quot;</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">6. Energy minimization of the solvated system</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">7. Position restrained MD</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=&gt; simulation broke down.</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=&gt; It is very probable that some molecule clashing with another.</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=&gt; since i have made sured that any atom of the ligands does not overlap on any atom of the protein with Visulization-software, </span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">      the clashed pair of the molecules are possible &quot; solvent vs solvent &quot;    or     &quot;solvent vs protein&quot;       or       &quot;solvent vs ligand &quot; </span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=&gt; however, from the Gromacs manual , command &quot;genbox&quot;</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">     &quot; Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less  </span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">     than the sum of the VanderWaals radii of both atoms. A database (<tt>vdwradii.<a href="http://manual.gromacs.org/current/online/dat.html">dat</a></tt>) of VanderWaals radii is read by the program, atoms not in the    </span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">     database are assigned a default distance <tt>-vdw</tt>.&quot;</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">=&gt;  here is    </span><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">vdwradii.dat  (the ligand is simply made of C, N, O, H)<br>
; Very approximate VanderWaals radii<br>; only used for drawing atoms as balls or for calculating atomic overlap.<br>; longest matches are used<br>; &#39;???&#39; or &#39;*&#39; matches any residue name<br>; &#39;AAA&#39; matches any protein residue name<br>
???  C     0.15<br>???  F     0.12<br>???  H     0.04<br>???  N     0.110<br>???  O     0.105<br>???  S     0.16<br></span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">My questions are </span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">1. anything wrong of my simulation procedures ?</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">2. how to find the clashed molecules ?   </span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">Thank you</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">Lin</span></div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>

<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: &#39;Times New Roman&#39;,&#39;serif&#39;; mso-fareast-font-family: &#39;Times New Roman&#39;; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"> </span></div>