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In molecular simulation (MD), one of the challenges is that the process interested occurs in the time scale which is out of the reach of normal MD. Rare events like protein fold, chemical reaction, which occur by crossing a very high barrier, are exaples. Many smart method were developed to enchance the sampling, such as umbrella sampling, replica exchange, conformational flooding and metadynamics etc. TPS is one of them and its advantage is to simulation the barrier crossing events (Transitions from one stable state to another stable state by crossing a very high barrier) without prior knowledge of the mechanism and the reaction rate constant can be evaluationed [1].
Much of the details of TPS has been explained in Peter Bolhuis's wetsite. There is a simple version of TPS for simulating the movement of one particle in a two-dimensional potential surface and it's worth for beginner trying. Since there are some mistakes there (Peter Bolhuis may not agree with me.), I have make some tiny changes. Peter have explained the way
to run the tutorial in detail and I am gonna here to show how to get the rate constant step by step.
We have implemented TPS into gromacs and then one can do TPS on very complex system. Here, we will provide the code and the manual to do TPS in gromacs. Via an example, we will also show the details of the commands.
This is the exercise shown in Peter Bolhuis's website, the extra details of how to do the exercise is presented here
A patch of gromacs for doing TPS is provided here and a brief manual proviede as well.
Two exaples are shown to explain how to use this patch in more details.
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