[gmx-users] Fixing periodicity effects on trajectory file

[Homa rooz]

Hi there
I'm working with gromacs for ligand-protein interaction simulation. I have
run MD for docked complex and now there is a problem with trajectory
visualization by VMD. The ligand has left binding site circulating around
the protein.
I tried to fix the problem by making index and extract the first frame from
the trajectory to use as  reference and also running "-center", "no jump",
"no pbc", "-fit rot" but the problem still exists. I'm quite confused.
Should I execute fixing command in the special order?
Which group is more preferred to be located at the center,Protein or
system(non-solvent)?
I would be grateful if you could help me in this matter.
-- 
Homa Ahmadi
Shahed University
Faculty of Basic Sciences
Alternative email> h.ahmadi at shahed.ac.ir <h.ahmadi at ast.ui.ac.ir>