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exercises:2019_uzh_acpc2:ex03 [2019/05/14 00:01] – keimreexercises:2019_uzh_acpc2:ex03 [2019/05/14 08:57] – jglan
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 where $s$ is the set CVs and $P(s)$ is the probability that the system has the set of CV values $s$. where $s$ is the set CVs and $P(s)$ is the probability that the system has the set of CV values $s$.
  
-The following Python script can be used to calculate the FES from the ''ch3f-COLVAR.metadynLog'' file produced by the MD run. (Don't forget to change the temperature!)+The following Python script can be used to calculate the FES from the ''ch3f-COLVAR.metadynLog'' file produced by the MD run. (Don't forget to change the temperature in Python script!)
  
 <code> <code>
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 kb = 8.6173303e-5 # eV * K^-1 kb = 8.6173303e-5 # eV * K^-1
  
-temperature = 1000.0+temperature = 1000.0                          #Change temperature according to your MD simulations!
 colvar_path = "./ch3f-COLVAR.metadynLog" colvar_path = "./ch3f-COLVAR.metadynLog"
  
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   * In general, how does potential energy differ from free energy? For our reaction, what are the activation barriers from the different free energy surfaces? How and why do they differ from the NEB barrier?   * In general, how does potential energy differ from free energy? For our reaction, what are the activation barriers from the different free energy surfaces? How and why do they differ from the NEB barrier?
 </note> </note>
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exercises/2019_uzh_acpc2/ex03.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1