[CP2K-user] [CP2K:20975] Wrong distance between geometrical centres and RMSD values reported in metadynLog

[Marcella Iannuzzi]

Hi Edwin, 

I think that the difference in the RMSD is due to the fact that in cp2k, if 
you do not specify weights, 
the displacements are weighted with the atomic masses in au units. 

Regards
Marcella

On Monday, December 16, 2024 at 2:49:16 AM UTC+1 helb... at gmail.com wrote:

> Sorry, I forgot to mention that there is no mention of RMSD units in 
> https://manual.cp2k.org/trunk/units.html
>
> On 12/16/24 1:47 AM, Edwin Helbert Aponte Angarita wrote:
> > Hi Albert,
> > 
> > You are right, the ratio between the distances measured on PyMOL and the 
> > COLVAR values reported in metadynLog is roughly 0.529, which is the 
> > conversion factor from Bohr and Angstrom. The PyMOL RMSD to COLVAR RMSD 
> > ratio tends towards 0.007 (see attached plot) but I can't figure out the 
> > units of RMSD in metadynLog.
> > 
> > Regards,
> > Edwin.
> > 
> > On 12/15/24 10:39 AM, Albert Makhmudov wrote:
> >> Hi Edwin,
> >>
> >> To the best of my knowledge, by default CP2K outputs everything in 
> >> a.u. but coordinates. Keeping that in mind, the distance between two 
> >> geometrical centers is c. 9-10 bohr which is roughly 4-5 angstrom. I’m 
> >> not sure about the RMSD values, though.
> >>
> >>
> >> Best,
> >>
> >> Albert
> >>
> >>> On Dec 14, 2024, at 21:27, Edwin Helbert Aponte Angarita 
> >>> <helb... at gmail.com> wrote:
> >>>
> >>> Dear All,
> >>>
> >>> I have been trying to calculate a free energy surface in the same way 
> >>> as presented in this tutorial:
> >>> https://www.cp2k.org/exercises:2020_uzh_acpc2:ex03
> >>> However, as collective variables I am specifying the distance between 
> >>> two geometrical centres and fitted RMSD to a reference structure. The 
> >>> calculation apparently runs fine but the values reported in 
> >>> metadynLog are wrong.
> >>>
> >>> I repeated the calculation using Clofenotane (DDT) as a test system 
> >>> so that I can post here my input files, which are attached. One of 
> >>> the CVs is the distance between the geometrical centre of the rings 
> >>> and the other is fitted RMSD to the initial structure. The distance 
> >>> reported in metadynLog is around 9angs while the one measured on 
> >>> PyMOL never goes above 5.5angs. RMSD values reported in metadynLog go 
> >>> up to around 160angs^2 while the value calculated on PyMOL never 
> >>> surpasses 1.7angs^2.
> >>>
> >>> Thank you in advance,
> >>>
> >>> Edwin.
> >>>
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> >>> <6WT_ideal.xyz><Clofenotane-COLVAR.metadynLog><FES-Clofenotane.inp>
> >>
>
>

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