[gmx-users] Protein moves out of box after several simulations, how to fix it?

Justin A. Lemkul jalemkul at vt.edu
Wed May 23 18:21:07 CEST 2012

On 5/23/12 5:30 PM, Marc Hömberger wrote:
> Hallo,
> I have several (12) simulations running in which I simulate a protein
> in a water box (cubic 9x9x9). For all simulations I can  see the
> following:
> After a few simulations (total time of 7.6ns) the protein moves out of
> the water box - for all the twelve simulations. Since the following
> simulation is started with the output .gro file of the prior
> simulation the protein moves further and further out of the box.  I
> have no idea if this is a problem because of periodic boundaries or if
> this is a problem with my vmd installation. Can anyone give me a hint
> what I could to to fix this and not have to restart all the runs?

Your observations are consistent with 100% normal (and expected) behavior. 
There is no "outside" of a periodic box.  Check out the first two bullet points 
here and the explanation that follows:


> I am using a script I used before and I am doing everything like last
> time but last time I did not see this behavior of the protein. I am
> using vmd to look at the protein and its trajectory (commands see
> below)

Whether or not a molecule stays near the perceived "center" of the unit cell is 
simply a matter of probability.  Given sufficient simulation time, all proteins 
in water will cross at least one periodic boundary.  Such is the nature of 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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