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--- exercises:common:mtd [2024/06/18 10:34] – [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 10: / Line 10: @@
   * Metadynamics simulation to trigger the replacement of an adsorbed formate/formic acid by a water molecule by following changes of two different collective variables.
+All relevant files can be downloaded {{ :exercises:common:tutorial_mtd.tar |here}}.
 ===== First task: dynamics of formic acid and water molecules on rutile (110) =====
@@ Line 87: / Line 88: @@
 Although no bias is added at this time, for each defined COLVAR an MTD variable is initialized. The [[https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/FREE_ENERGY/METADYN/PRINT/COLVAR.html | PRINT/COLVAR]] section controls the printing of the COLVAR output file, which contains, among other information, the instantaneous values of the CVs (second and third columns) at the indicated time, in fs (first column).
-By plotting the instantaneous values of the CVs along the 10 ps MD run, the amplitude of the equilibrium fluctuations can be evaluated and then used to set up the size of the Gaussian hills that build up the biasing potential during the MTD simulation. With the NN and ND values of 8 and 12, respectively, the first CV fluctuates close to 1, with an amplitude smaller than 0.3, whereas the second one fluctuates close to 0, with an amplitude of approximately 0.05. This indicates that this specific formate has some freedom to move away from the surface, but without fully desorbing. As a consequence, the free water molecule is not able to get close to the titanium site, which explains the low fluctuation amplitude in the second CV.
+By plotting the instantaneous values of the CVs along the 10 ps MD run, the amplitude of the equilibrium fluctuations can be evaluated and then used to set up the size of the Gaussian hills that build up the biasing potential during the MTD simulation. With the NN and ND values of 8 and 12, respectively, the first CV fluctuates close to 1, with an amplitude smaller than 0.2, whereas the second one fluctuates close to 0, with an amplitude of approximately 0.05. This indicates that this specific formate has some freedom to move away from the surface, but without fully desorbing. As a consequence, the free water molecule is not able to get close to the titanium site, which explains the low fluctuation amplitude in the second CV.
 ===== Second task: metadynamics of the dynamic equilibrium between formic acid and water on rutile (110) =====
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 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: