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

Mark Abraham mark.j.abraham at gmail.com
Tue May 13 15:57:38 CEST 2014


I would expect there is no way to do this with g_cluster. g_cluster -h
should mention it if it did exist. The only way to implement it is to
iterate over all permutations of equivalent molecules. That's doable, but
it would have to have been implemented deliberately.


On Tue, May 13, 2014 at 1:27 PM, Gil Rutter <g.o.rutter at warwick.ac.uk>wrote:

> 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
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