<p>Hi Afsaneh,</p>
<p>The PBC and the .gro file format are explained in the manual, chapter 3.<br>
The last line of the .gro file has the box stored as</p>
<p>XX YY ZZ XY XZ YX YZ ZX ZY</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Mar 5, 2011 6:03 AM, "afsaneh maleki" <<a href="mailto:maleki.afsaneh@gmail.com">maleki.afsaneh@gmail.com</a>> wrote:<br><br>Hi,<br><br>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif"">I want to
create <span></span>*.gro file with simulation box size as
following:<span> </span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>3.4604674520000<span> </span>0.000000000000<span> </span>0.000000000000</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>1.7302337260000<span> </span>2.9968527222000<span> </span>0.000000000000</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>0.000000000000<span> </span><span> </span><span> </span>0.000000000000<span> </span><span> </span><span> </span>10.0000000000</span></p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif"">I
used the command:</span><span style="font-size:12pt;line-height:115%"></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif"">]editconf <span> </span>–f *.pdb<span>
</span><span> </span>–o *.gro <span> </span><span> </span>–box 3.46
<span> </span>3.46 <span> </span> 10.<span> </span><span> </span><span> </span>–c <span> </span><span> </span>–angle
<span> </span>90 <span> </span>90 <span> </span>60</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""> are these commands proper to create this </span><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif"">simulation box size?</span><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>system size :<span>
</span>4.975<span> </span>2.951<span> </span>0.084 (nm)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>center<span>
</span>:<span> </span>0.025<span> </span>0.548<span>
</span>0.966 (nm)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>box vectors :<span> </span>0.000<span>
</span>0.000<span> </span>0.000 (nm)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>box angles<span>
</span>:<span> </span>0.00<span> </span>0.00<span>
</span>0.00 (degrees)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>box volume<span>
</span>:<span> </span>0.00<span> </span>(nm^3)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>shift<span>
</span>:<span> </span>2.570<span> </span>0.951<span>
</span>4.034 (nm)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif"">new center<span> </span>:<span>
</span>2.595<span> </span>1.498<span> </span>5.000 (nm)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif"">new box vectors
:<span> </span>3.460<span>
</span>3.460 10.000 (nm)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif"">new box
angles<span> </span>:<span>
</span>90.00<span> </span>90.00<span> </span>60.00 (degrees)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif"">new box
volume<span> </span>: 103.68<span> </span>(nm^3)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif"">Also I paste
some .gro file</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>1<span>
</span>NAU<span> </span>39<span> </span>1.759<span>
</span>1.647<span> </span>4.998</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>1<span>
</span>HAC<span> </span>41<span> </span>1.855<span>
</span>1.618<span> </span>4.993</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>1<span>
</span>HAB<span> </span>40<span> </span>1.686<span>
</span>1.578<span> </span>5.002</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:150%"><span style="font-size:12pt;line-height:150%;font-family:"Times New Roman","serif""><span> </span>3.46000<span>
</span>2.99645 <span> </span><span> </span>10.00000<span>
</span>0.00000<span> </span>0.00000<span> </span>1.73000<span>
</span><span style="color:rgb(255, 0, 0)">0.0000 -0.0000 -0.00000</span></span></p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%"> </span></p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif"">What is three last values in box
vector,<span style="color:rgb(255, 0, 0)">0.00 -0.00 -.0</span></span><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif";color:rgb(255, 0, 0)"> </span><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif""><span style="color:rgb(255, 0, 0)">0</span>?</span></p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif""></span></p><br><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif"">Would one please clear me about these vectors?</span></p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif""> </span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif"">3.46000<span> </span>2.99645 <span> </span><span> </span>10.00000<span>
</span>0.00000<span> </span>0.00000<span> </span>1.73000<span>
</span><span style="color:rgb(255, 0, 0)">0.0000 -0.0000 -0.00000</span></span></p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif"">xx
<span> </span>yy<span> </span>zz<span> </span>?<span> </span>?<span> </span>xy<span> </span>?<span> </span>?<span> </span>?</span></p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif""><br></span></p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif"">I
have another question that </span><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif"">does g_hbond has the
compatibility with non-cubic (or parallelpiped) cells?</span></p>
<br clear="all"><br>good luck<br><font color="#888888">Afsaneh <br><br>
</font><br>--<br>
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