[gmx-users] Influence from images (PBC)
xieyh at hkusua.hku.hk
Tue Feb 21 02:21:53 CET 2006
By using periodic boundary condition, images are existing. If I am not totally wrong, images should have some influence on our simulation, right?
Now, in my simulation, a solute is solvated in the water with a small box. I doubt that images have certain unexpected influence due to the small size of simulated box. My question is how to eliminate the influence from images?
As known, we can set mdp file with pbc=no to represent the case without periodic boundary. Somebody can tell me what is the detailed meaning of pbc=no, and what should be the values for cutoff rvdws, rcoulomb and rlist?
Besides, what is the difference between pbc=xyz and pbc=full except that the later denote the case of infinite molecule?
Thanks very much.
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