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| Main Authors: | , , |
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| Format: | Preprint |
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2024
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| Online Access: | https://arxiv.org/abs/2412.03448 |
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| _version_ | 1866913667450142720 |
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| author | Asthagiri, Dilipkumar N. Parambathu, Arjun Valiya Beck, Thomas L. |
| author_facet | Asthagiri, Dilipkumar N. Parambathu, Arjun Valiya Beck, Thomas L. |
| contents | Earlier we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step $δt \leq 0.5$ fs to ensure equipartition between translational and rotational modes. Here we extend 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 examine integration time-steps ranging from $0.5$ fs to $4.0$ fs for various thermostat plus barostat combinations. We find that a small $δt$ 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, and the dielectric constant, a measure of dipole moment fluctuations, are also seen to be sensitive to $δt$. Using the mean volume estimated from the $NpT$ simulation, we examine 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 $δt$. In going from $δt = 2$ fs to $δt = 0.5$ 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2412_03448 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | 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. Parambathu, Arjun Valiya Beck, Thomas L. Soft Condensed Matter Chemical Physics Earlier we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step $δt \leq 0.5$ fs to ensure equipartition between translational and rotational modes. Here we extend 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 examine integration time-steps ranging from $0.5$ fs to $4.0$ fs for various thermostat plus barostat combinations. We find that a small $δt$ 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, and the dielectric constant, a measure of dipole moment fluctuations, are also seen to be sensitive to $δt$. Using the mean volume estimated from the $NpT$ simulation, we examine 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 $δt$. In going from $δt = 2$ fs to $δt = 0.5$ 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. |
| title | Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein |
| topic | Soft Condensed Matter Chemical Physics |
| url | https://arxiv.org/abs/2412.03448 |