exercises:common:mtd
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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 | ||
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* Metadynamics simulation to trigger the replacement of an adsorbed formate/ | * Metadynamics simulation to trigger the replacement of an adsorbed formate/ | ||
+ | All relevant files can be downloaded {{ : | ||
===== First task: dynamics of formic acid and water molecules on rutile (110) ===== | ===== First task: dynamics of formic acid and water molecules on rutile (110) ===== | ||
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Although no bias is added at this time, for each defined COLVAR an MTD variable is initialized. The [[https:// | Although no bias is added at this time, for each defined COLVAR an MTD variable is initialized. The [[https:// | ||
- | 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, | + | 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, |
===== Second task: metadynamics of the dynamic equilibrium between formic acid and water on rutile (110) ===== | ===== 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:// | The printing of the HILLS file is controlled by [[https:// | ||
- | The provided | + | The resulting |
Finally, by using this information, | Finally, by using this information, |
exercises/common/mtd.1718706864.txt.gz · Last modified: 2024/06/18 10:34 by fnunes