Enhanced sampling of transition states
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland
- Department of Physics, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland
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.
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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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
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28 February 2019 [This version]