Victor Rosas Garcia
rosas.victor at gmail.com
Fri Nov 7 14:52:32 CET 2014
That is the first thing I would do: make the box larger, so the total
pulling distance is less than half the box length.
2014-11-06 23:40 GMT-06:00 Yixin Ai <aixintiankong at 126.com>:
> 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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