Jayashrita Debnath^1*, Michele Parrinello^1*, 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]

Publication date: Feb 14, 2020

How to cite this record

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

Materials Cloud sections using this data

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.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

External references

Keywords

Molecular Modelling Transition States Enhanced Sampling Critical Clusters Nucleation