Re: [gmx-users] dodecahedron box

On 1/2/13 7:03 AM, Turgay Cakmak wrote: Dear gromacs users, I am trying to solvate several peptides (at a desired positions) in a dodecahedron box. I have done following steps; 1) editconf -f peptides.gro -o peptides_nb.gro -c -d 1.0 -bt dodecahedron 2) genbox -cp peptides_nb.gro

Re: [gmx-users] dodecahedron box

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

[gmx-users] dodecahedron box

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