AMBER Archive (2002)

Subject: a water jumps

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Mon Jul 29 2002 - 22:47:21 CDT

Hi All,
 
  I still have a trouble on MD simulation with an error message, "The systen has extended byhond the extent of the virtual box". I prepared a protein and a ligand. Solvent waters were added with solvatecap command with WATBOX216 in tleap. Radius of the sphere of solvent waters was 28 A, whose center was an atom of the ligand. Then, all residues with in 10 A from any atom of the ligand and all solvent waters were specified as movable residues, all others were fixed with BELLY option. In MD, a water molecule close to boundary moved about 13 A to vacuum area in 5 ps. This water molecule caused the error, I think. Then, the question is why the water molcule moved such a lot. Please give me any clue!
 
Masaki Tomimoto