Re: [gmx-users] Questions about dodecahedron box

Thanks, Tsjerk. Exactly as what you said, it was because split of molecules over the boundary. It runs smoothly right now as I started with a dodecahedron box. best, Zhenlong On Thu, Oct 6, 2011 at 12:24 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Zhenlong, I guess that some molecules

[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,

Re: [gmx-users] Questions about dodecahedron box

Hi Zhenlong, I guess that some molecules got split 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 zxl1...@gmail.com wrote: Dear