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.par...@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 > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
