[gmx-users] smd

Yixin Ai aixintiankong at 126.com
Fri Nov 7 06:40:37 CET 2014

Dear everyone,
    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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