Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein"

Asthagiri, Dilipkumar N; Valiya Parambathu, Arjun; Beck, Thomas L

doi:10.13139/OLCF/2480346

Title: Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein"

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Abstract

Previously, we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step dt that is less than or equal to 0.5 fs to ensure equipartition between translational and rotational modes. We extended that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examined integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small time-step, dt, is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, is seen to be sensitive to dt. Using the mean volume estimated from the NpT simulation, we examined the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to dt. In going from a time-step of 2 fs to a time-step of 0.5 fs, the change inmore »« less

Authors:

Asthagiri, Dilipkumar N; Valiya Parambathu, Arjun; Beck, Thomas L

Oak Ridge National Laboratory
University of Delaware, Newark

Publication Date:: Thu Dec 12 00:00:00 UTC 2024

DOE Contract Number:: AC05-00OR22725

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: Office of Science (SC)

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 74 ATOMIC AND MOLECULAR PHYSICS; 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY

OSTI Identifier:: 2480346

DOI:: https://doi.org/10.13139/OLCF/2480346

Citation Formats


                    Asthagiri, Dilipkumar N, Valiya Parambathu, Arjun, and Beck, Thomas L. Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein".  United States: N. p., 2024. 
        Web.  doi:10.13139/OLCF/2480346.

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                    Asthagiri, Dilipkumar N, Valiya Parambathu, Arjun, & Beck, Thomas L. Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein".  United States.  doi:https://doi.org/10.13139/OLCF/2480346

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                    Asthagiri, Dilipkumar N, Valiya Parambathu, Arjun, and Beck, Thomas L. 2024.  
"Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein"".  United States.  doi:https://doi.org/10.13139/OLCF/2480346.  https://www.osti.gov/servlets/purl/2480346. Pub date:Thu Dec 12 00:00:00 UTC 2024

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@article{osti_2480346,

  title        = {Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein"},

  author       = {Asthagiri, Dilipkumar N and Valiya Parambathu, Arjun and Beck, Thomas L},

  abstractNote = {Previously, we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step dt that is less than or equal to 0.5 fs to ensure equipartition between translational and rotational modes. We extended that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examined integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small time-step, dt, is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, is seen to be sensitive to dt. Using the mean volume estimated from the NpT simulation, we examined the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to dt. In going from a time-step of 2 fs to a time-step of 0.5 fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein. The data-set contains the simulation metadata and log files that support the claims noted above.},

  doi          = {10.13139/OLCF/2480346},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Thu Dec 12 00:00:00 UTC 2024},

  month        = {Thu Dec 12 00:00:00 UTC 2024}

}

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DOI: https://doi.org/10.13139/OLCF/2480346

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