[gmx-users] Assignment of Atoms to Charge Groups in x2top

[darrellk at ece.ubc.ca]

Hi All,
I am wondering how atoms are assigned to charge groups when a .gro file
is run through x2top. I have a structure in a .gro file where not all
the atoms in sequential order are adjacent to one another, yet x2top
seems to assign them to the same charge group. For example, atoms 1301
to 1348 are assigned to the same charge group yet only atoms 1301 to
1324 are adjacent to one another and atoms 1325 to 1348 are adjacent to
one another but atoms 1301-1324 are separated by a distance of 5 nm from
atoms 1325-1348 and clearly they should not be assigned to the same
charge group.

Thanks or your help.

Darrell