[gmx-users] g_cluster: treating identical molecules as interchangeable

[Gil Rutter]

Hi all,

In a simulation of, say, 2 units of the same molecule, it would be useful
if g_cluster could treat the two molecules as being interchangeable.

For example, if molecule A has three atoms at coordinates C1, C2 and C3,
and identical molecule B has three atoms at coordinates C4, C5 and C6, this
frame would be clustered with a second frame in which molecule B is at C1,
C2 and C3 and molecule A is at C4, C5 and C6. (Indeed, in this case the
RMSD would be 0.)

Hopefully that makes sense. Is there any way to achieve this in g_cluster?

Best regards,

Gil Rutter