AmericanChemicalSociety.com

In the second year of research under the support of the PRF award, the research group led by the PI has continued on developing the adaptive force matching (AFM) method as outlined in the proposal. New functionalities have been incorporated in the AFM code developed under the PRF support. We have also proceeded to develop force field for methane clathrate and calculate the melting temperatures as described in the proposal.

Continued development of the AFM method: The AFM method uses Molecular Mechanics (MM) to sample the configuration space and rely on QM (Quantum Mechanics)/MM methods to obtain forces. In AFM, The MM model used during sampling and QM/MM calculations are iteratively improved to match the high quality QM method. The AFM method was first tested to create a force field for water. Systematic analysis of the forces predicted by the AFM models revealed a deficiency in the standard point charge expression short range columbic interactions. The simple point charge model over-estimates electrostatic interactions when the charge-charge separation is small. This manifests itself leading to over-attractive hydrogen bonds in water.  We employed a short-range shifted-and-truncated power-law potential to address such an over-attraction. This short-range potential was able to significantly reduce the root mean square error (RMSE) of the fit thus significantly improve the quality of the water model. Before we proceed with creating a potential for methane clathrate, we systematically studied other terms routinely used in various water models. This was done since the AFM method can provide a systematic way of assessing the importance of force field terms. In this past two years, two manuscripts have been published reporting our work in developing and refining the AFM method. One of them was the 4^th most downloaded article on JCP for the month it was published. Two more manuscripts are in preparation, one of them summarizes our work in determining the best set of force field expressions that produce the highest quality water potential without unduly large computational cost.  The other one reports our determination of high quality force field for methane-water mixture.

Free energy determination through non-equilibrium simulations: We proposed to use the non-equilibrium free energy simulation method with Jarzynski's identity to estimate the free energy difference between methane clathrate and methane bubble in water. This work is currently close to be completed by graduate student Gerrick Lindberg. Before determining the free energy difference between methane clathrate and hydrated methane bubble, we surveyed current methods for non-equilibrium free energy simulation. We found most existing studies were not performed following an optimal protocol so that the simulation efficiency was far from optimal. In order to achieve our goal of quick determination of free energy differences between various phases of methane hydrate. We investigated the probability of improving the efficiency of standard non-equilibrium free energy determination techniques. Using the fluctuation and dissipation theorem estimate for the rate for dissipative work generation as a function of the switching speed, we created a scheme where the switching speed is adjusted on-the-fly during the simulation so that the rate for dissipative work generation remains a constant. This produces a switching profile that spend more time in regions where the dissipative work generation is fast but less time in regions where irreversibility is negligible. This work has published on the Journal of Chemical Physics.

Currently, we are applying the methods developed under the support of PRF to finalize the calculations free energies of various phases of methane clathrate.  This work will be published in the years to follow. The PRF award helped us to generate preliminary results for securing an NSF Career grant.

Omololu Akin-ojo, who had been supported by this award and had contributed significantly to the project, recently continued on as an independent post-doctoral faculty at ICTP in Italy. Gerrick Lindberg, who was also supported by this award, is in his fifth year of graduate study. He is well on its way to graduation. Most of his thesis work is supported by this award. Building on the progress made possible by this award, Gerrick is expected to publish a few more papers on the thermodynamic stability of methane clathrate and graduate next year.