Molecular Dynamics Simulations with Enhanced Sampling

This tutorial will lead you step by step to do molecular dynamics (MD) simulations with enhanced sampling using Qbics. Assume you have read Standard Molecular Dynamics Simulations, Geometry Optimization, Density Functional Theory Calculations or Molecular Mechanics Calculations.

Although standard MD is very important, it may take too long for a system to go across high barriers to enable the occurance of chemical reactions or large amplitute motions. Such processes are called rare events. To enable us to sample the rare events in short time-scale, we need to add bias potentials on some collective coordinates to accelerate specific processes. This is the so-called enhanced sampling MD. In Qbics, such algorithms are implmented in Plumed library. As long as you have ever learned Plumed, you can use all its functions combined with DFT, semi-empirical, MM or QM/MM methods in Qbics. You just need add plumed_fn in md...end, enhaned sampling will be automatically activated:

md
    plumed_fn pl.dat
end

where pl.dat is the name of the file that gives Plumed settings like:

pl.dat

d1:  DISTANCE ATOMS=319,320
PRINT ARG=d1 STRIDE=100 FILE=COLVAR

For a complete tutorial of Plumed, please refer to: https://www.plumed.org/doc-v2.9/user-doc/html/index.html.

Molecular Dynamics Simulations with Enhanced Sampling

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Example: XXXXXX 