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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Nov 30 18:40:04 CET 2009

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.



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

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