Enhanced sampling of transition states

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{
  "updated": "2020-02-14T00:00:00+00:00", 
  "metadata": {
    "edited_by": 98, 
    "contributors": [
      {
        "familyname": "Debnath", 
        "affiliations": [
          "Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi  13, CH-6900, Lugano, Switzerland"
        ], 
        "givennames": "Jayashrita", 
        "email": "debnathj@student.ethz.ch"
      }, 
      {
        "familyname": "Parrinello", 
        "affiliations": [
          "Department of Chemistry and Applied Biosciences, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi  13, CH-6900, Lugano, Switzerland"
        ], 
        "givennames": "Michele", 
        "email": "parrinello@phys.chem.ethz.ch"
      }, 
      {
        "familyname": "Invernizzi", 
        "affiliations": [
          "Department of Physics, ETH Zurich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900, Lugano, Switzerland"
        ], 
        "givennames": "Michele"
      }
    ], 
    "owner": 9, 
    "title": "Enhanced sampling of transition states", 
    "conceptrecid": "105", 
    "id": "107", 
    "license": "Creative Commons Attribution 4.0 International", 
    "doi": "10.24435/materialscloud:2019.0010/v2", 
    "mcid": "2019.0010/v2", 
    "_oai": {
      "id": "oai:materialscloud.org:107"
    }, 
    "status": "published", 
    "version": 2, 
    "keywords": [
      "Molecular Modelling", 
      "Transition States", 
      "Enhanced Sampling", 
      "Critical Clusters", 
      "Nucleation"
    ], 
    "publication_date": "Feb 14, 2020, 00:00:00", 
    "references": [
      {
        "citation": "J. Debnath, M. Invernizzi, M. Parrinello, arXiv preprint,  arXiv:1812.09032 ", 
        "url": "https://arxiv.org/abs/1812.09032", 
        "doi": "", 
        "comment": "Preprint where the method and a few of its applications are discussed.", 
        "type": "Preprint"
      }, 
      {
        "citation": "J. Debnath, M. Invernizzi, M. Parrinello, J. Chem. Theory Comput. 15, 4 (2019), 2454-2459", 
        "url": "https://pubs.acs.org/doi/full/10.1021/acs.jctc.8b01283", 
        "doi": "10.1021/acs.jctc.8b01283", 
        "comment": "Paper in which the method is explained and the results are discussed.", 
        "type": "Journal reference"
      }
    ], 
    "license_addendum": "", 
    "is_last": true, 
    "_files": [
      {
        "checksum": "md5:3459dbeff368678fc6e45d2444d0c27a", 
        "key": "readme.txt", 
        "description": "Description of all the files", 
        "size": 897
      }, 
      {
        "checksum": "md5:d6aed6a3a4377bc6a9be3fd5997b05f4", 
        "key": "Enhanced_TS_Data_v2.zip", 
        "description": "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\r\nTD_TS-target-plumed2.6.cpp         :  The code implementing the method described. It is a part of the VES module of PLUMED version 2.6\r\nsn2.inp               :  cp2k input file for SN2 reaction\r\ninput.lmp        :  LAMMPS input file for the condensation case\r\ninput                 :  Plumed input file for the double well potential case\r\npot_coeffs_input.data :  The double well potential\r\nPlumed.dat                       :  Plumed input file used for running TS-Target simulations ( Double well potential case) using VES\r\n", 
        "size": 14081
      }
    ], 
    "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."
  }, 
  "id": "107", 
  "revision": 1, 
  "created": "2020-05-12T13:52:36.043273+00:00"
}