aixintiankong at 126.com
Fri Nov 7 06:40:37 CET 2014
i want to use gromacs to perform the steered molecular dynamcs simulation. My system is the protein-ligand complex in the center of the box an i want to pull out of the ligand form the protein ative site. i have set the pbc in my mdp file. However, after simulation, i find that the ligand out of the box and get into the next unit cell. How does this make sense? should i the box larger to keep the liand in the original unit cell?
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