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:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
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
diffusion.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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