Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof

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{
  "metadata": {
    "is_last": true, 
    "version": 1, 
    "title": "Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof", 
    "keywords": [
      "metadynamics", 
      "flying Gaussian method", 
      "molecular dynamics simulation", 
      "sampling"
    ], 
    "description": "Biomolecular simulations have a great potential in protein engineering, drug discovery and many other fields. Unfortunately, this method is computationally expensive, so many interesting processes cannot be routinely studied. In order to address this problem we developed Flying Gaussian method [Journal of Chemical Theory and Computation 12, 4644-4650 (2016)]. This method simultaneously simulates multiple replicas of the studied system and disfavor replicas with similar structures by artificial bias potential. The question arises how to calculate an unbiased free energy surface from a biased simulation. This dataset demonstrates together with mathematical arguments supports application of Umbrella Sampling reweighing method, despite the fact that this method is designed for methods with a time-independent bias potential.\r\n", 
    "license": "Creative Commons Attribution 4.0 International", 
    "references": [
      {
        "url": "", 
        "type": "Journal reference", 
        "citation": "P. K\u0159\u00ed\u017e, Z. \u0160u\u0107ur, V. Spiwok, Journal of Physical Chemistry B 121, 10479-10483 (2017)", 
        "comment": "Paper in which we show that free energy surface from flying Gaussian method (Journal of Chemical Theory and Computation 12, 4644-4650 (2016)) can be calculated by umbrella sampling reweighing.", 
        "doi": "10.1021/acs.jpcb.7b09337"
      }
    ], 
    "doi": "10.24435/materialscloud:2019.0013/v1", 
    "conceptrecid": "112", 
    "publication_date": "Apr 17, 2019, 00:00:00", 
    "edited_by": 100, 
    "_oai": {
      "id": "oai:materialscloud.org:113"
    }, 
    "contributors": [
      {
        "affiliations": [
          "University of Chemistry and Technology, Prague"
        ], 
        "email": "spiwokv@vscht.cz", 
        "familyname": "Spiwok", 
        "givennames": "Vojtech"
      }, 
      {
        "affiliations": [
          "University of Chemistry and Technology, Prague"
        ], 
        "email": "sucurz@vscht.cz", 
        "familyname": "\u0160u\u0107ur", 
        "givennames": "Zoran"
      }, 
      {
        "affiliations": [
          "University of Chemistry and Technology, Prague"
        ], 
        "email": "krizp@vscht.cz", 
        "familyname": "K\u0159\u00ed\u017e", 
        "givennames": "Pavel"
      }
    ], 
    "owner": 299, 
    "license_addendum": "", 
    "mcid": "2019.0013/v1", 
    "_files": [
      {
        "size": 1170993, 
        "checksum": "md5:4acf8cde64782dcea61e991f091129f7", 
        "description": "Input files (input structure, topology, Plumed input) for a simple simulation used to demonstrate that free energy surface can be calculated from Flying Gaussians results using Umbrella Sampling reweighing, despite the dynamic nature of the bias potential. Tested on OpenMPI4.0.0, Gromacs 2018.5 and Plumed2.5.0. Script provided.", 
        "key": "flyinggaussian2.zip"
      }, 
      {
        "size": 1240, 
        "checksum": "md5:f6727be8f7a558b4bb390642de346027", 
        "description": "README.txt file with descriptions.\r\n", 
        "key": "README.txt"
      }
    ], 
    "id": "113", 
    "status": "published"
  }, 
  "revision": 2, 
  "updated": "2021-01-26T14:42:32.616967+00:00", 
  "created": "2020-05-12T13:52:40.776367+00:00", 
  "id": "113"
}