Step number range for FES calculation from RESTART file

[Mawuli]

Hi all,

I'm currently analyzing data from my ab initio well-tempered metadynamics simulations, where I deposit hills every 50 steps (NT_HILLS), using a time step of 0.5 fs.

I have a couple of questions regarding the free energy surface (FES) calculation using the graph.psmp tool in CP2K:

1. Step Range for FES Calculation:
Is it possible to specify a range of step numbers (e.g., from a particular step to another) when calculating the FES using graph.psmp?

2. Effect of Changes in Atom in CVs:
One of the atoms used in my collective variables (CVs) changes during the simulation. Specifically, atom 322 — a proton from a water molecule — is exchanged with another proton over time. Will this affect the resulting fes.dat file?

&colvar # 1
&coordination
atoms_from 3
atoms_to 18  
r0 [angstrom] 2.0
nn 6
nd 12
&end coordination
&end colvar

&colvar # 2
&coordination
atoms_from 18
atoms_to 322  ## This atom is a proton from water which is exchanged with another proton  
r0 [angstrom] 1.5
nn 6
nd 12
&end coordination
&end colvar

&colvar # 3
&coordination
atoms_from 3
atoms_to 2  
r0 [angstrom] 2.0
nn 6
nd 12
&end coordination
&end colvar

3. If colvar3 does change so much can i plot the fes as 

graph.psmp -cp2k -file $Restart_file -ndim 3 -ndw 1  2 -out $FES

Any advice or suggestions would be greatly appreciated.
Thank you!

Mawuli