[gmx-users] periodic boundary conditions

Lianqing Zheng lzheng at me.rochester.edu
Thu Dec 2 16:31:16 CET 2004

Dear GMX-pals,

I have questions on how Gromacs deals with PBC for molecules. For example, 
for a water molecule H1-O-H2 with only H2 out of simulation box, if H2 is
moved back to the box by periodic boundary conditions, then the O-H2
bonded will be distorted. How does Gromacs deal with this?

Thanks a lot!


More information about the gromacs.org_gmx-users mailing list