Tutorials

Basic run

The umbrella sampling 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-umb.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: umb
   
   ndim: 2
   x0:
   - 18.0
   - 18.0
   mass: 1.0
   potential: Mueller2d
   
   biases:
   - umb
   umb_k: 0.1
   umb_n: 1
   umb_r0:
   - 18
   - 18
   
   method: md
   integrate: 2nd-langevin
   md_gamma: 0.01
   temperature: 300.0
   dt: 1.0
   steps: 20000
   
   oneplot: true
   plot: true
   movie: false
   screen: true
   plot_boundary:
   - - 0.0
     - 48.0
   - - 0.0
     - 40.0
   
   dump: true
   dump_freq: 10
   track_pvf: true
   
   stat_freq: 10
   

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

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

   unlike metadynamics, the fix0.dat do not store any information because the harmonic penalty function is a constant.

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

   

4. the arguments and equations see Harmonic

Tunning the parameters

1. k

Post Processing