[CP2K-user] [CP2K:20969] Wrong distance between geometrical centres and RMSD values reported in metadynLog

[Edwin Helbert Aponte Angarita]

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 
>>> <helbert2a 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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