[gmx-users] dodecahedron box

[Tsjerk Wassenaar]

Hi Zahra,

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.

Cheers,

Tsjerk

On Dec 28, 2011 7:42 AM, "Zahra M" <s_zahra_mousavi at yahoo.com> wrote:

hi dear all users
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.
1) How can I implement this exact distance from the other protein and also
the edges of the box?
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.
I don't know what to do, please help me.
thank you in advanced.

-zahra

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