Re: [gmx-users] Solvating dodecahedron

Tsjerk Wassenaar wrote: Hi Justin, Note that the pseudo-sphere representation is for visualization purposes only; the triclinic cell should be the input for any simulation. This not true. It doesn't matter which representation you use as input. Molecules may be broken over PBC, but the topo

Re: [gmx-users] Solvating dodecahedron

Hi Justin, > Note that the pseudo-sphere representation is for visualization > purposes only; the triclinic cell should be the input for any simulation. This not true. It doesn't matter which representation you use as input. Molecules may be broken over PBC, but the topological information is tak

Re: [gmx-users] Solvating dodecahedron

shivangi nangia wrote: Hello All, I am trying to solvate a protein sitting in a dodecahedron using genbox. It gets solvated but a box of solvent is created around the protein. I want the protein to be sitting in a dodecahedron filed with solvent. I used the following commands: editconf -f

[gmx-users] Solvating dodecahedron

Hello All, I am trying to solvate a protein sitting in a dodecahedron using genbox. It gets solvated but a box of solvent is created around the protein. I want the protein to be sitting in a dodecahedron filed with solvent. I used the following commands: editconf -f onlyhis.gro -bt dodecahedro