I am trying to do metadynamics simulation for my protein. Can someone explain what is a collective variable, and on what basis we decide collective variables in a metadynamics run?
Thanks.
The reaction coordinate used to enhance the fluctuation in metadynamics. The gaussian potential (hill) is added on this reaction coordinate. This variable should describe the slow motion in the process of interest, and no other slow motions should exist. Otherwise, you need to add reaction coordinates to describe other slow motions in order to achieve convergence in normal ns simulations.
Try the tutorials of metadynamics at https://plumed.github.io/doc-v2.4/user-doc/html/_syntax.html.
For a new user I would recommend to run umbrella sampling first, as there are a number of tricks in metadynamics.
The reaction coordinate used to enhance the fluctuation in metadynamics. The gaussian potential (hill) is added on this reaction coordinate. This variable should describe the slow motion in the process of interest, and no other slow motions should exist. Otherwise, you need to add reaction coordinates to describe other slow motions in order to achieve convergence in normal ns simulations.
Try the tutorials of metadynamics at https://plumed.github.io/doc-v2.4/user-doc/html/_syntax.html.
For a new user I would recommend to run umbrella sampling first, as there are a number of tricks in metadynamics.
Metadynamics belongs to a class of methods in which sampling is facilitated by the introduction of an additional bias potential (or force) that acts on a selected number of degrees of freedom, often referred to as collective variables (CVs).
It is a low-dimensional (1, 2 or 3 usually) projection of the high-dimensional (6N) space of MD simulations.
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