[gmx-users] periodic boundary condition

[Dallas Warren]

Kass

> > the boundary.  But when I run gromacs on my system, some atoms are out 
> of the
> > simulation box.

Just so it is clear, GROMACS writes out the files as a default such that 
the center of a molecule is within the simulation box.  However, a section 
of the molecule can actually be protruding out of the box, which is 
especially evident with long chain molecules.  During calculations though, 
these are still corrected considered where they enter the other side of the 
box.  Just for visualisation it is much better to have a complete molecule 
rather than it split over the boundaries.

If you happen to have molecules over the boundaries then trjconv and 
editconf can be used to center them etc.

A very handy feature that the visualisation program VMD now has is the 
displaying of the pbc boxes in the +-x,y & z directorions.  Great if you 
have aggregates of molecules forming.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083