Enhanced sampling of transition states

Authors: Jayashrita Debnath1*, Michele Parrinello1*, Michele Invernizzi2

  1. Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland
  2. Department of Physics, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland
  • Corresponding authors emails: debnathj@student.ethz.ch, parrinello@phys.chem.ethz.ch

DOI10.24435/materialscloud:2019.0010/v2 (version v2, submitted on 14 February 2020)

How to cite this entry

Jayashrita Debnath, Michele Parrinello, Michele Invernizzi, Enhanced sampling of transition states, Materials Cloud Archive (2020), doi: 10.24435/materialscloud:2019.0010/v2.

Description

The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods are able to obtain sufficient sampling in order to draw the free energy, the transition states are often sparsely sampled. We propose an approach based on the Variationally Enhanced Sampling Method to enhance sampling in the transition region. To this effect, we introduce a dynamic target distribution which uses the derivative of the instantaneous free energy surface to locate the transition regions on the fly and modulate the probability of sampling different regions. Finally, we exemplify the effectiveness of this approach in enriching the number of configurations in the transition state region in the cases of a chemical reaction and of a nucleation process.

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Files

File name Size Description
readme.txt
MD5MD5: 3459dbeff368678fc6e45d2444d0c27a
897 Bytes Description of all the files
Enhanced_TS_Data_v2.zip
MD5MD5: d6aed6a3a4377bc6a9be3fd5997b05f4
13.8 KiB TD_TS-target-plumed2.4.cpp : The code implementing the method described. It is a part of the VES module of PLUMED version 2.4
TD_TS-target-plumed2.6.cpp : The code implementing the method described. It is a part of the VES module of PLUMED version 2.6
sn2.inp : cp2k input file for SN2 reaction
input.lmp : LAMMPS input file for the condensation case
input : Plumed input file for the double well potential case
pot_coeffs_input.data : The double well potential
Plumed.dat : Plumed input file used for running TS-Target simulations ( Double well potential case) using VES

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.

External references

Preprint (Preprint where the method and a few of its applications are discussed.)
Journal reference (Paper in which the method is explained and the results are discussed.)

Keywords

Molecular Modelling Transition States Enhanced Sampling Critical Clusters Nucleation

Version history

14 February 2020 [This version]

28 February 2019