From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Nov 25 2021 - 10:47:29 CST
Dear Alexey,
I think the problem is that this script was written under the assumption
that you're operating at a residue level, and thus, that there aren't
repeated residue entries in the second argument to rmsd_residue_over_time
(given the function name, one would not expect the user to give multiple
atoms from the same residue in the function argument). If such entries do
exist, it is going to behave oddly because the loops in that function act
over the list of residues passed will then be repeatedly adding to the
residue level rmsd, and then dividing by it. Now, that script *should* have
been written defensively and passed the residue id list through [lsort
-unique ...] prior to acting on it, but as it is, there is a clear
deviation in your input from what the function is expecting.
Best,
Peter
On Thu, Nov 25, 2021 at 4:02 AM Alexei Rossokhin <
alrossokhin_at_remove_yahoo.com> wrote:
> Dear NAMD users,
> While browsing the NAMD tutorial I found the residue_rmsd.tcl script to
> calculate RMSD for individual residues. When I tried to run it, the
> results puzzled me a little.
>
> When I used the selection "protein and chain A and resid 174 and name CA
> and noh" for my MD calculations I got the following result
>
> RMSD of residue 174 is 1.3978458595465855
> Average rmsd per residue: 1.3978458595465855
>
> When I used the selection "protein and chain A and resid 174 and name CA
> CB CG CD and noh" I got the following result
>
> RMSD of residue 174 is 5.591383438186342
> RMSD of residue 174 is 0.022276428040583034
> RMSD of residue 174 is 8.875070932503201e-5
> RMSD of residue 174 is 3.535884833666614e-7
> Average rmsd per residue: 1.4034372426311832
>
> Using "protein and chain A and resid 174 and name CB and noh" I got
>
> RMSD of residue 174 is 1.3978458595465855
> Average rmsd per residue: 1.3978458595465855
>
> If to run the script separately for CA or CB result is the same. If to
> run the script with the selection "name CA CB CG CD", the result for
> individual atoms is strange, although the average is close in all cases.
>
> What does it mean, any bug in the script?
> Thank you for help.
>
> Alexey
>
> PS I attached the residue_rmsd.tcl script.
>
>
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