Hello, I am a beginner in molecular dynamics, and am considering to use Metadynamics to address one of the questions about protein structure in my research. I would appreciate if the RG community could help me in understanding the MTD parameters.
1) Higher gaussian height would enhance the sampling or not? (My understanding: No)
2) Does frequency of deposition of Gaussian effect the sampling? Also, do short intervals mean longer simulation time to explore a given conformational space?
3) In unbiased simulations, we judge convergence by seeing if the RMSD stabilized. How do we judge convergence in metadynamics?
4) My understanding is that higher bias explores more conformational space. Is that right? If yes, what is the advantage of lower bias over higher bias in a well-tempered metadynamics?
5) how to decide the initial Gaussian height?
Would greatly appreciate your response.
Thanks.
Hello Rajiv Lakkaniga
Here are some basic understandings of meta-dynamics simulation
1. The collective variables determination is more important than Gaussian Height.
2. The higher Gaussian Height (H) will decrease simulation duration, i.e., decrease conformational sampling.
3. Decrease in H will increase simulation duration i.e., more detail about conformational sampling and space exploration.
4. The initial Gaussian height can (0.05kcal/mol), to decide the duration of the simulation to reach the equilibrium and after that frequency of the addition Gaussian (T_G) 0.09ps can be tuned as per your computational resources(power) and details want to explore.
5. The convergence can be judged based on free-energy calculations for each frame(g_mmpbsa)/free-energy surface to know about energy minima.
6. Conformational space/equilibrium exploration will be limited by the Wall (25 Å for distance) parameter, it can be tuned for more exploration.
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