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/v1 (version v1, submitted on 28 February 2019)

How to cite this entry

Jayashrita Debnath, Michele Parrinello, Michele Invernizzi, Enhanced sampling of transition states, Materials Cloud Archive (2019), doi: 10.24435/materialscloud:2019.0010/v1.

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
Enhanced_TS_Data.zip
MD5MD5: c7973e016f2532e7a9d1152f981f5ea6
8.8 KiB
TS-target.cpp : The code implementing the method described. It is a part of the VES module of PLUMED version 2.4
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
readme.txt
MD5MD5: f2398db83d378cbbacafdcfa7bf9bad0
749 Bytes Description of all the files

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.)
J. Debnath, M. Invernizzi, M. Parrinello, arXiv preprint, arXiv:1812.09032

Keywords

Transition States Nucleation Critical Clusters Enhanced Sampling Molecular Modelling

Version history

28 February 2019 [This version]