<html><body><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><div><br></div><div>-zahra<br></div></div></body></html>