[gmx-users] Center of simulation box

Dear all, In my simulation, when the simulation box shrinks, the center of box always shift towards the origin even if the center motion is set to removed every timestep. I just wonder if there is an anticipated center position for a given simulation box in gromacs. The box type is dodecahedron in

Re: [gmx-users] Questions about dodecahedron box

plit over the boundaries during > equilibration. You have to make them whole before changing the box. > Better to start off with a rhombic dodecahedron though. > > Cheers, > > Tsjerk > > On Thu, Oct 6, 2011 at 6:29 PM, zhenlong li wrote: > > Dear all, > > My syste

[gmx-users] Questions about dodecahedron box

Dear all, My system is based on Martini, needs a dodehedron box. Initially, it was minimized and equilibrated with a cubic box smoothly. Then I used the follow command to translate the box in to dodehedron: editconf -f f0.gro -bt dodecahedron -d 2 -o vesdode.gro But with this change,