Tutorials

Basic run

The metadynamics run basic is similar to plain molecular dynamics run, except for additional arguments to define the biases.

1. Run a demo example.

   ndsimulator examples/2d-mtd.yaml
   

   The yaml file can be found on the github repo or as shown below. We will explain the arguments one by one in the following section.

   root: ./reference
   run_name: mtd
   
   ndim: 2
   potential: Mueller2d
   x0:
   - 22.0
   - 30.0
   mass: 1.0
   
   method: md
   temperature: 300
   integration: langevin
   gamma: 0.1
   steps: 100000
   dt: 1.0
   
   biases:
   - mtd
   mtd_biasf: 10.0
   mtd_dep_freq: 100
   mtd_sigma:
   - 2.0
   - 2.0
   mtd_w: 0.05
   
   plot: true
   plot_bias: true
   oneplot: true
   plot_boundary:
   - - 0.0
     - 48.0
   - - 0.0
     - 40.0
   plot_ebound:
   - -1.4
   - 0.2
   plot_freq: 10
   plot_increment:
   - 1.0
   - 1.0
   movie: false
   
   dump: true
   dump_freq: 1000
   
   verbose: debug
   

2. With the arguments root: ./reference and run_name: mtd, the call will generate a folder in reference/mtd

   ls reference/mtd/
   $ colvar.dat  fix0.dat  force.dat  log  oneplot.png  pos.dat  thermo.dat  velocity.dat
   

   the additional fix0.dat file store the indices, locations (x, y), and height of the deposited gaussian biases in the order of index bias_x bias_y sigma_x sigma_y w`

3. The simulation result is automatically visualized in the oneplot.png

   

4. the arguments and equations see Gaussian

Tunning the parameters

1. deposition

Post Processing