[gmx-users] PBC - Protein and Ligands

Steven Neumann s.neumann08 at gmail.com
Wed Feb 29 18:01:24 CET 2012

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

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?

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