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

[Tsjerk Wassenaar]

Hi Daniel,

If the structure is correct in the coordinate file you used as input
to generate the .tpr, you can use that structure as reference to
trjconv, using -pbc nojump.

Cheers,

Tsjerk

On Mon, Nov 30, 2009 at 6:17 PM, Daniel Parton
<daniel.parton at bioch.ox.ac.uk> wrote:
> 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
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist