Hi Edwin, <div><br /></div><div>I think that the difference in the RMSD is due to the fact that in cp2k, if you do not specify weights, </div><div>the displacements are weighted with the atomic masses in au units. </div><div><br /></div><div>Regards</div><div>Marcella<br /><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, December 16, 2024 at 2:49:16 AM UTC+1 helb...@gmail.com wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Sorry, I forgot to mention that there is no mention of RMSD units in
<br><a href="https://manual.cp2k.org/trunk/units.html" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/units.html&source=gmail&ust=1734530095049000&usg=AOvVaw0m5WD3Mg1JFweSBCcE8mTy">https://manual.cp2k.org/trunk/units.html</a>
<br>
<br>On 12/16/24 1:47 AM, Edwin Helbert Aponte Angarita wrote:
<br>> Hi Albert,
<br>>
<br>> You are right, the ratio between the distances measured on PyMOL and the
<br>> COLVAR values reported in metadynLog is roughly 0.529, which is the
<br>> conversion factor from Bohr and Angstrom. The PyMOL RMSD to COLVAR RMSD
<br>> ratio tends towards 0.007 (see attached plot) but I can't figure out the
<br>> units of RMSD in metadynLog.
<br>>
<br>> Regards,
<br>> Edwin.
<br>>
<br>> On 12/15/24 10:39 AM, Albert Makhmudov wrote:
<br>>> Hi Edwin,
<br>>>
<br>>> To the best of my knowledge, by default CP2K outputs everything in
<br>>> a.u. but coordinates. Keeping that in mind, the distance between two
<br>>> geometrical centers is c. 9-10 bohr which is roughly 4-5 angstrom. I’m
<br>>> not sure about the RMSD values, though.
<br>>>
<br>>>
<br>>> Best,
<br>>>
<br>>> Albert
<br>>>
<br>>>> On Dec 14, 2024, at 21:27, Edwin Helbert Aponte Angarita
<br>>>> <<a href data-email-masked rel="nofollow">helb...@gmail.com</a>> wrote:
<br>>>>
<br>>>> Dear All,
<br>>>>
<br>>>> I have been trying to calculate a free energy surface in the same way
<br>>>> as presented in this tutorial:
<br>>>> <a href="https://www.cp2k.org/exercises:2020_uzh_acpc2:ex03" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://www.cp2k.org/exercises:2020_uzh_acpc2:ex03&source=gmail&ust=1734530095049000&usg=AOvVaw27OTq0Hh8Jd9XZ-vzCsIbK">https://www.cp2k.org/exercises:2020_uzh_acpc2:ex03</a>
<br>>>> However, as collective variables I am specifying the distance between
<br>>>> two geometrical centres and fitted RMSD to a reference structure. The
<br>>>> calculation apparently runs fine but the values reported in
<br>>>> metadynLog are wrong.
<br>>>>
<br>>>> I repeated the calculation using Clofenotane (DDT) as a test system
<br>>>> so that I can post here my input files, which are attached. One of
<br>>>> the CVs is the distance between the geometrical centre of the rings
<br>>>> and the other is fitted RMSD to the initial structure. The distance
<br>>>> reported in metadynLog is around 9angs while the one measured on
<br>>>> PyMOL never goes above 5.5angs. RMSD values reported in metadynLog go
<br>>>> up to around 160angs^2 while the value calculated on PyMOL never
<br>>>> surpasses 1.7angs^2.
<br>>>>
<br>>>> Thank you in advance,
<br>>>>
<br>>>> Edwin.
<br>>>>
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<br>>>> cp2k/0b7d866a-d3f3-4fda-904a-d8633db2ba2a%<a href="http://40gmail.com" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://40gmail.com&source=gmail&ust=1734530095049000&usg=AOvVaw3AN5uoMoXF4sGq0N4Bgv6F">40gmail.com</a>.
<br>>>> <6WT_ideal.xyz><Clofenotane-COLVAR.metadynLog><FES-Clofenotane.inp>
<br>>>
<br>
<br></blockquote></div>
<p></p>
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