[CP2K-user] [CP2K:21364] Understanding the COLVAR file

[James Hanson]

Good morning CP2K community,
I have been attempting some metadynamics studies for the reaction of 
carbonic acid (H2CO3) on a surface of portlandite (Ca(OH)2) when in a phase 
of humid CO2. I set three CVs as follows:
1.) Coordination between the carbon atom of my H2CO3 (indexed as atom "88") 
and all Calcium atoms
2.) The z-axis distance between the carbon atom of my H2CO3 and the nearest 
layer of Calcium atoms (I simply chose one of these Calciums, indexed 179)
3.) Coordination between the carbon atom of my H2CO3 and any surrounding 
hydrogens.
Note, I only want exploration of the first CV (i.e. bond formation of the 
), hence I have set lambda = 1 for CV1, lambda=0 for CV2, and lamba=0.005 
for CV3 (not equal to 0 as the H2CO3 will lose it's hydrogens in order to 
react with the calcium). I have also imposed a wall on CV2 such that if the 
H2CO3 drifts too far from the surface it will be repelled back. 

I ran an NVT for 3000 steps (timestep=1fs) with no issues. And the first 
step of my *-COLVAR.metadynLog is as follows: 
3001.00000000     0.00022663    13.55591332     2.83252720     0.00022504   
 13.55217251     2.82544777    -0.00000159     0.00000000    -0.00003540   
  0.00000000     0.00000000     0.00000000     0.00000000***************   
  0.00000000    -0.00000000     0.00019718    -0.00000000     0.00000013   
  0.00000000***************   373.00000000
I am very confused to what these numbers mean, would someone please explain 
what I am looking at here? For instance, the 2nd to 4th numbers appear to 
be the instantaneous values of my CVs? However, what are then the 5th to 
7th, why do they appear similar? Moreover, why is the temperature listed as 
a perfect 373 K, even though *.ener is fluctuating around 373K (and rightly 
so!)?

After 1431 steps, the latest print is: 
   4431.00000000     0.00034802    25.20968437     2.93700752     
0.00034484    13.10788947     2.94859093    -0.00000473    -0.00000000     
0.00005719    -0.00000182     0.05079545    -0.00083906     0.00000000     
0.00000000     0.00000000    -0.00000004     0.00019715    -0.00000352     
0.00000033     0.00846389     0.00000000   373.00000000
Take note of CV2: 25.20968437 Bhor == 13.34 Ang. This number is alarming as 
it would imply that my H2CO3 has jumped the wall I positioned at 20 Bohr 
(as seen in my input file). However, upon inspection of the atomic 
structure, I can see that atom 88 has not drifted at all by 13.34 
Angstroms. In fact, CV2's actual instantaneous value is much closer to the 
value in column 6:  13.10788947  == 6.93 Ang (the value displayed in my 
screenshot is 7.07 Ang because it is an absolute distance measurement as 
opposed to purely just along the z-axis). What is happening here, which 
numbers in the .metadynLog should i read as my CVs?? Thank you in advance...

Signed,
A very confused man...


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