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 style=""></span>*.gro file with simulation box size as
following:<span style=""> </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 style=""> </span>3.4604674520000<span style=""> </span>0.000000000000<span style=""> </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 style=""> </span>1.7302337260000<span style=""> </span>2.9968527222000<span style=""> </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 style=""> </span>0.000000000000<span style=""> </span><span style=""> </span><span style=""> </span>0.000000000000<span style=""> </span><span style=""> </span><span style=""> </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 style=""> </span>–f *.pdb<span style="">
</span><span style=""> </span>–o *.gro <span style=""> </span><span style=""> </span>–box 3.46
<span style=""> </span>3.46 <span style=""> </span> 10.<span style=""> </span><span style=""> </span><span style=""> </span>–c <span style=""> </span><span style=""> </span>–angle
<span style=""> </span>90 <span style=""> </span>90 <span style=""> </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 style=""> </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 style=""> </span>system size :<span style="">
</span>4.975<span style=""> </span>2.951<span style=""> </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 style=""> </span>center<span style="">
</span>:<span style=""> </span>0.025<span style=""> </span>0.548<span style="">
</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 style=""> </span>box vectors :<span style=""> </span>0.000<span style="">
</span>0.000<span style=""> </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 style=""> </span>box angles<span style="">
</span>:<span style=""> </span>0.00<span style=""> </span>0.00<span style="">
</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 style=""> </span>box volume<span style="">
</span>:<span style=""> </span>0.00<span style=""> </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 style=""> </span>shift<span style="">
</span>:<span style=""> </span>2.570<span style=""> </span>0.951<span style="">
</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 style=""> </span>:<span style="">
</span>2.595<span style=""> </span>1.498<span style=""> </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 style=""> </span>3.460<span style="">
</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 style=""> </span>:<span style="">
</span>90.00<span style=""> </span>90.00<span style=""> </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 style=""> </span>: 103.68<span style=""> </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 style=""> </span>1<span style="">
</span>NAU<span style=""> </span>39<span style=""> </span>1.759<span style="">
</span>1.647<span style=""> </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 style=""> </span>1<span style="">
</span>HAC<span style=""> </span>41<span style=""> </span>1.855<span style="">
</span>1.618<span style=""> </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 style=""> </span>1<span style="">
</span>HAB<span style=""> </span>40<span style=""> </span>1.686<span style="">
</span>1.578<span style=""> </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 style=""> </span>3.46000<span style="">
</span>2.99645 <span style=""> </span><span style=""> </span>10.00000<span style="">
</span>0.00000<span style=""> </span>0.00000<span style=""> </span>1.73000<span style="">
</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 style=""> </span>2.99645 <span style=""> </span><span style=""> </span>10.00000<span style="">
</span>0.00000<span style=""> </span>0.00000<span style=""> </span>1.73000<span style="">
</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 style=""> </span>yy<span style=""> </span>zz<span style=""> </span>?<span style=""> </span>?<span style=""> </span>xy<span style=""> </span>?<span style=""> </span>?<span style=""> </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>Afsaneh <br><br>