[gmx-users] trjconv - PBC

Steven Neumann s.neumann08 at gmail.com
Mon Oct 24 14:45:35 CEST 2011

Dear Gmx Users,

I am trying to convert my trajectory using trjconv.  My system is made of 10
ligands and protein. Protein is jumping
divided into parts. The same is with my ligands. I am confused about the
point 2 and 3:

2. Extract the first frame from the trajectory as reference for removing
jumps if you want to remove jumps.

Which option of trjconv is responsible for extraction of my 1st frame?

3. Remove jumps if you want to have them removed using the first frame

trjconv -f traj.xtc -s *.tpr -pbc nojump (how to use 1st frame here
extracted from previous point?)

I would be really thankful!

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