[gmx-users] how gromacs calculate center of mass for broken molecules?

[chris.neale at utoronto.ca]

That depends. mdrun pull code does it smartly via pull_pbcatom  
(assuming that you have chosen pull_pbcatom and your box size  
smartly), while g_dist is not smart about it at all. Can you be more  
specific about what you want to do?

-- original message --

Hi everyone:

How gromacs calculate center of mass for broken molecules? If the molecule
is broken due to the pbc, where will the center of mass be?

Thanks,
Kun