[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Ok, I guess in future I will have to make sure the box is big enough to contain the entire vesicle in the triclinic representation. It's kind of a shame though, as the main reason for using the rhombic dodecahedron box was to minimize the amount of bulk solvent required. Thanks for your help t

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi, I've tried using trjconv -pbc nojump with a .tpr created from the first frame of the trajectory (clustered so the vesicle should be whole). The output trajectory starts with a complete vesicle, but small numbers of lipid particles progressively move to places outside of the box. By the en

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi, Thanks for the suggestion to use trjconv -pbc nojump. Unfortunately, it has not worked, as the vesicle is still not whole in the trajectory. I have tried subsequently centering the trajectory, and representing the system with -ur compact, but still it does not work. I am wondering if the

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

as a .gro file and the program is run on that file only. Does anyone have any idea how to get this to work? Any help would be much appreciated! Please let me know if you need more information about my simulation set-up. Daniel Parton -- gmx-users mailing listgmx-users@gromacs.org