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--- exercises:common:mtd [2024/06/18 10:40] – [First task: dynamics of formic acid and water molecules on rutile (110)] fnunes
+++ exercises:common:mtd [2024/06/18 10:51] (current) – [Second task: metadynamics of the dynamic equilibrium between formic acid and water on rutile (110)] fnunes
@@ Line 136: / Line 136: @@
 The printing of the HILLS file is controlled by [[https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/FREE_ENERGY/METADYN/PRINT/HILLS.html | PRINT/HILLS]], with the information given in the following order: timestep, coordinates of the center in the CV space for CV1, coordinates of the center in the CV space for CV2, width of CV1, width of CV2, and height of the hill.
-The provided trajectory is about 34 ps long and shows the desorption of one formate as formic acid, with subsequent adsorption of a water molecule to the freed titanium site. Additionally, in this case, we added a reflective wall after around 17 ps of simulation, which prevents the desorbed formic acid from moving too far from the surface. Other quantities can be monitored from the [[https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/FREE_ENERGY/METADYN/PRINT/COLVAR.html | PRINT/COLVAR]] output file, in the following order: timestep, the instantaneous value of CV1, the instantaneous value of CV2, the instantaneous gradient of the bias potential computed wrt CV1, the instantaneous gradient of the bias potential computed wrt CV2, instantaneous gradient wrt CV1 of wall potentials (if present), instantaneous gradient wrt CV2 of wall potentials (if present), the instantaneous value of the bias potential, instantaneous values of the wall potentials (if present).
+The resulting trajectory is about 34 ps long and shows the desorption of one formate as formic acid, with subsequent adsorption of a water molecule to the freed titanium site. Additionally, in this case, we added a [[https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/FREE_ENERGY/METADYN/METAVAR/WALL.html|reflective wall]] after around 17 ps of simulation, which prevents the desorbed formic acid from moving too far from the surface. Other quantities can be monitored from the [[https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/FREE_ENERGY/METADYN/PRINT/COLVAR.html | PRINT/COLVAR]] output file, in the following order: timestep, the instantaneous value of CV1, the instantaneous value of CV2, the instantaneous gradient of the bias potential computed wrt CV1, the instantaneous gradient of the bias potential computed wrt CV2, instantaneous gradient wrt CV1 of wall potentials (if present), instantaneous gradient wrt CV2 of wall potentials (if present), the instantaneous value of the bias potential, instantaneous values of the wall potentials (if present).
 Finally, by using this information, the FES can be reconstructed with the help of the graph script available with cp2k, in the //tools// directory. The command line, in this case, would look as follows: