[gmx-users] How to apply trjconv -nojump to a part of a system

Trayder Thomas trayder.thomas at monash.edu
Thu Jul 11 03:51:51 CEST 2013

VMD might do what you want with the PBC tools plugin (installed by
default). http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
unwrap being the equivalent of -nojump

Otherwise, couldn't you just view your 2 trajectories simultaneously, one
with protein the other not?


On Wed, Jul 10, 2013 at 9:13 AM, Bin Liu <fdusuperstring at gmail.com> wrote:

> Hi All,
> For the convenience of visualization, I need to remove the jump of one
> component (say a protein) of the system at the boundary. I don't need to,
> or say I need not to remove the jump of the other components (say a lipid
> bilayer), since otherwise the system will look falling apart. I noticed I
> can cluster a part of a system, then output all the atoms in the system in
> which only the part is clustered, and the other components unchanged. Does
> GROMACS have similar function when *-nojump* is used?
> If this can not be accomplished directly, is there a way to circumvent it?
> I figured out a way, but haven't implemented it. I can plug the coordinates
> of the protein treated with *-nojump* into the trajectory of the whole
> system which is not treated with *-nojump*. It is kind of substituting the
> coordinates of one component in one trajectory with the coordinates of the
> same component in another trajectory. Is there anyone aware of a tool or a
> script to do this job?
> Thank you very much.
> Regards
> Bin
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