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

[Shanjie Huang]

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
constrains. 

Thanks.

 
-- 
  Shanjie Huang
  suibingkuai at 123mail.org

-- 
http://www.fastmail.fm - A no graphics, no pop-ups email service