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

Bin Liu fdusuperstring at gmail.com
Wed Jul 10 01:13:00 CEST 2013

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.



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