Re: [gmx-users] pulling with dodecahedral box

Hi Mareike, Probably your simulation starts off with remapping your pull-atom over the periodic boundaries. Make sure that the atom and the protein are properly placed inside the rhombic dodecahedron (actually the brick representation of it) before the simulation. Note that Gromacs performs mappi

[gmx-users] pulling with dodecahedral box

Hallo! I have got a question on the afm pulling option. I am trying to pull a single atom into the direction of the center of mass of a protein in my simulation cell. Everything works fine with a cubic box. When I use a truncated dodecahedral box, at time step 1 the atom is suddenly located at