From: Vermaas, Joshua (
Date: Thu Aug 29 2019 - 20:25:40 CDT

Ok, next question, what did you align against? The "RMSD_after_alignment.png" looks ok, assuming that you aligned against the *last* frame instead of the *first* frame like Maestro did. RMSD measures against a specific reference state, and the implementations should give the same result, you just need to make sure that the reference state and the comparison states are equivalent.


On 2019-08-29 18:13:05-06:00 I. Camps wrote:

The values are very different. I am attaching here a PNG image with both curves.
I am not aware about the Maestro methodology used to calculate RMSD, but, thinking in this possibility, I did an alignment in VMD. The figure is also attached. The result is very different too.

On Thu, Aug 29, 2019 at 7:40 PM Vermaas, Joshua <<>> wrote:
How different is different? Changes in the 5th or 6th digit after the decimal point may be due to accumulated round-off errors based on the different order of additions or algorithmic implementation differences. If its larger than that, I suspect you are measuring two different quantities. VMD's RMSD plugins depend on the alignment to be done first, whereas Maestro *might* (?) use the QCP algorithm, which doesn't need an alignment.


PS I can't recall any image or other attachments coming through in the past, so I'm guessing no?

On 2019-08-29 12:37:21-06:00<> wrote:

Dear all,
I am newbie using VMD.
My first task was to calculate the RMSD from a Molecular Dynamics done using DESMOND.
I obtained the C-alpha and ligand RMSD using Maestro interface and using the plug-in withing VMD.
The problem I am facing is that the results are different.
In the case of C-alpha, in both programs (Maestro and VMD), the selection was: "backbone and name CA".
In the case of ligand, in Maestro it is just to select ligand. In VMD, the ligand is identify as "UNK" residue.
Also, in both cases, the reference frame is the frame "0".
What I am doing wrong?

PS: I sent a previous email to this list with a figure attached. Does this list accept attachments?