[gmx-users] PBC - Protein and Ligands

Vedat Durmaz durmaz at zib.de
Wed Feb 29 18:17:17 CET 2012

i always did it (successfully) with one single command:

trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n 


Am 29.02.2012 18:01, schrieb Steven Neumann:
> Dear Gmx Users,
> I am run a simulation with Gromacs 4.5.4. of my protein and 15 
> ligands. The problem I face is PBC which I cannot get rid of. I used:
> 1.First make your molecules whole if you want them whole (system).
> trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.xtc
> 2.Cluster your molecules/particles if you want them clustered
> 3.Extract the first frame from the trajectory as reference for 
> removing jumps if you want to remove jumps.
> trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb
> 4.Remove jumps if you want to have them removed using the first frame 
> (system)
> trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc
> So the trajecory of my ligands is smooth but they do do bind to the 
> different periodic images. As i know it is impossible to obtain the 
> proper trajectory of all of them I just want to obtain the realistic 
> final positions of my system to extract pdb file for further umbrella 
> sampling. Any suggestions?
> Steven
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