[gmx-users] trjconv - Protein and jumping ligands

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 30 15:02:43 CEST 2011

Steven Neumann wrote:
> Dear Gromacs Users,
> To avoid pbc in my trajectory file I used command:
> trjconv -f md.trr -s md.tpr -pbc mol -ur compact -center -o md.xtc
> I have choosen protein to be centered. Everything is ok with my protein 
> which does not jump and remains centered in the box. However, some of my 
> ligands change their place in given frame VERY rapidly... I had the 
> situation like this before the command above with my protein as 
> well which now is stable... Any suggestions please?

I posted a link earlier to the proper workflow.  Dealing with protein-ligand 
complexes can be tricky, since the COM of the protein may be reset to the center 
of the box but the COM of the ligand is still across a periodic boundary.  You 
may have to center on a custom index group somewhere else in the protein or 
center on the ligand itself to get a reasonable representation.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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