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

[Daniel Parton]

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 problem lies with the initial frame. I don't understand very well 
the geometrical theories for how it is possible to represent a rhombic 
dodecahedron as a triclinic box, so I'm relying only on what I see when 
viewing the system with VMD. But looking at the first frame, it appears 
to be impossible for the vesicle to be whole in the triclinic box. After 
converting with trjconv -ur compact, the system appears as expected - 
the vesicle is whole and centered, with a shell of water around it, 
extending to the edges of the rhombic dodecahedron box.

So my feeling is that although the vesicle appears to be whole when 
viewed with the compact representation, it is impossible to make the 
vesicle whole in the triclinic representation, as certain dimensions of 
the box are too small. Just as further explanation, I think that if the 
box:vesicle size ratio was larger, then it should be possible to fit the 
whole vesicle in the triclinic box. Thus trjconv -pbc nojump does not 
help, as the vesicle is not whole in the first (or any) frame. Does this 
make sense, and would it seem likely to be the problem? And if so, could 
there be a way around this problem?

Regards,

Daniel