<p>Hi Zahra,</p>
<p>You could first create rectangular boxes for each of the two, using -d 0.5 Then translate one over the first box vector length of the other (along x: editconf -translate). Put the two coordinate sets together and generate a rhombic dodecahedron for the combined set.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Dec 28, 2011 7:42 AM, "Zahra M" <<a href="mailto:s_zahra_mousavi@yahoo.com">s_zahra_mousavi@yahoo.com</a>> wrote:<br><br><div><div style="color:#000;background-color:#fff;font-family:garamond,new york,times,serif;font-size:14pt">
<div>hi dear all users</div><div>I'm simulating 2 proteins in a dodecahedron unit cell,and I want to put these 2 proteins in an exact distance from each other, and also from the boundaries, and I have some questions for doing this.</div>
<div>1) How can I implement this exact distance from the other protein and also the edges of the box?</div><div>2) when I use dodecahedron unit cell with this command: "editconf -f protein.gro -o protein_newbox.gro -bt dodecahedron -d 1.0 -c", the first protein is in the center of the box, but as I want to add the second protein at the distance of 1.0 nm from the first one, I decided to determine box vectors and protein position myself, and I wrote: "editconf -f protein.gro -o protein_newbox.gro -box 4 4 6 -angles 60 60 90 -center 2 2 2", but a part of protein becomes outside the boundaries. I've
examined the other numbers for -box vectors and -center, but the result was the same.</div><div>I don't know what to do, please help me.</div><div>thank you in advanced.</div><font color="#888888"><div><br></div><div>
-zahra<br></div></font></div></div><br>--<br>
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