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" <[email protected]> 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
