[gmx-users] Why my protein always falls out of the water box?

Shanjie Huang suibingkuai at 123mail.org
Mon Mar 13 14:49:36 CET 2006

Hi dear friends,
I performed a molecular dynamics of a ligand-receptor complex for 5ns;
but I found that my complex always fall out from the water box quickly
in the first 1ns. What may be the problem? 
Can I constrain some residues which are far away from the active site to
aviod this problem? But I am worry about the extra constrain would
interfere my MD result, for in the normal situation there should be no


  Shanjie Huang
  suibingkuai at 123mail.org

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