[gmx-users] simulation box shape and length

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 15 15:00:13 CEST 2012

On 6/15/12 8:47 AM, tarak karmakar wrote:
> Dear All,
>         I am little unaware of choosing the shape and length of box while
> simulating protein in water. I saw in one of the GROMACS tutorials [
> http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water] in which
> they have kept the protein at the center of the box and the distance from any
> atom of the protein to the wall of the box as 1.2 nm. [ r_cut off = 0.8 nm ] . I
> got the reason for the selection of box length but_*still not clear about the
> shape of the box.
> *What is the relation between the shape of the box and the computational cost?*

You can save a lot of computational time using a suitable box shape.  For a 
globular protein like the one in the tutorial, a cubic box is far less efficient 
than a rhombic dodecahedron or truncated octahedron.  The choice of box shape 
should be dictated by the inherent symmetry of the system.  For membranes, a 
rectangular or cubic box is appropriate.  For proteins, it's usually a waste. 
These topics are discussed in the manual, section 3.2.



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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