VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
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"

-Josh

On 2019-05-07 18:00:52-06:00 owner-vmd-l_at_ks.uiuc.edu 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”?

Previous related posts:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/10201.html
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17002.html

Thanks,
Patrick