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

MGiò magiofer at gmail.com
Mon Mar 13 15:23:17 CET 2006

Hi you!
it may not be as bad as it looks like. Usually the one happening to your
protein is only a visualization problem, if an atom of your protein crosses
the periodic simulation box, it might appear as if the whole molecule jumps
out of the box, because the coordinates of one of its periodic images are
shown instead of those referring to the real box. You can simply assess if
this is the case by running a single step dynamics, at a low temperature, if
the protein jumps out all the same, it can't be because of the real protein
movement! In this case, you can just convert you trajectory by
trjconv -center -pbc whole
this way you should have a trajectory in which your protein quietly stays in
its box.
hope it helps!


On 3/13/06, Shanjie Huang <suibingkuai at 123mail.org> wrote:
> 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
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