From: Vermaas, Joshua (
Date: Tue May 07 2019 - 19:11:08 CDT

Hi Patrick,

In VMD 1.9.3, there is a sparsely documented alternative algorithm that *does* take the order parameter. Try "measure rmsd_qcp $sel $ref order $orderlist"


On 2019-05-07 18:00:52-06:00 wrote:
Hi all,

Is anyone aware if an atom order parameter been implemented for the “measure rmsd” command, or if there is a workaround for trajectories that does not involve manually reordering atoms in the file?

Perhaps there is a way to get the RMSD directly from “measure fit”?

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