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Biased molecular dynamics

The biased molecular dynamics can be considered as a special type of metadynamics in which the bias potential is provided by the user at the beginning of the simulation and is not updated afterwards. The setup for the biased molecular dynamics should contain the following items:
  1. set the standard MD-related flags: IBRION=0, TEBEG, POTIM, NSW
  2. set MDALGO to 11 or 21 for the simulation with an Andersen, or Nose-Hoover thermostat, respectively (check description of ANDERSEN_PROB and SMASS for the thermostat-specific setting)
  3. in order to avoid updating of the bias potential, set HILLS_BIN to the value of NSW for the current simulation
  4. define collective variables in ICONST (see Sec. 6.62.4), the input parameter STATUS for collective variables must be set to 5
  5. define the bias potential in file PENALTYPOT, see Sec. 6.62.4
The values of all collective variables for each MD step are listed in file REPORT, check the lines after the string "Metadynamics".


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Next: Constrained molecular dynamics Up: Performing the simulations Previous: Metadynamics   Contents   Index
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