[CP2K-user] [CP2K:20976] Wrong distance between geometrical centres and RMSD values reported in metadynLog

[Edwin Helbert Aponte Angarita]

Hi Marcella,

Thank you for your reply, I did not know that they were weighed by 
default, it is not mentioned here 
https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/RMSD.html

Regards,
Edwin.

On 12/17/24 3:04 PM, Marcella Iannuzzi wrote:
> 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 <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 <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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>      >>> cp2k/0b7d866a-d3f3-4fda-904a-d8633db2ba2a%40gmail.com
>     <http://40gmail.com>.
>      >>> <6WT_ideal.xyz><Clofenotane-COLVAR.metadynLog><FES-
>     Clofenotane.inp>
>      >>
> 
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