[gmx-users] simulation box shape and length

tarak karmakar tarak20489 at gmail.com
Fri Jun 15 14:47:37 CEST 2012

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

*Any help in this regard would be highly appreciated.*
* Thanks


*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809 *
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