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arXiv · 2308.08383

Equilibration between Translational and Rotational Modes in Molecular Dynamics Simulations of Rigid Water Requires a Smaller Integration Time-Step Than Often Used

Dilipkumar N. Asthagiri·Thomas L. Beck
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Abstract

In simulations of aqueous systems it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time-step $δt$ for integrating the equations of motion. Thus $δt = 2$ fs is often used in simulating rigid models of water. We simulate the SPC/E model of water using $δt$ from 0.5 fs to 3.0 fs. We find that for all but $δ= 0.5$ fs, equipartition between translational and rotational modes is violated: the rotational modes are at a lower temperature than the translation modes. The autocorrelation of the velocities corresponding to the respective modes shows that the rotational relaxation occurs at a time-scale comparable to vibrational periods, invalidating the original assumption for freezing vibrations. $δt$ also influences thermodynamic properties: the mean system potential energies are not converged until $δt = 0.5$ fs, and the excess entropy of hydration of a soft, repulsive cavity is also sensitive to $δt$.

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Dilipkumar N. Asthagiri, Thomas L. Beck. 2023-08-16. Equilibration between Translational and Rotational Modes in Molecular Dynamics Simulations of Rigid Water Requires a Smaller Integration Time-Step Than Often Used. https://arxiv.org/abs/2308.08383

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