Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: All-atom molecular dynamics simulations re used to predict water-cyclohexane distribution coefficients \(D_{cw}\) of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules re parameterized with the transferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies re computed by an established protocol using windod alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error in \(\log D_{cw}\) of almost 4 log units and an overall signed error of −3 compared to experimental data. There was no substantial overall difference in accuracy beten simulating in NVT and NPT ensembles. The signed error suggests a systematic error but the experimental \(D_{cw}\) data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations.
['Ian M. Kenney', 'Oliver Beckstein', 'Bogdan I. Iorga']
I am writing a research paper on a idea Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field
[{"from": "human", "value": "I am writing a research paper on a idea Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field"}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: All-atom molecular dynamics simulations re used to predict water-cyclohexane distribution coefficients \\(D_{cw}\\) of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules re parameterized with the transferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies re computed by an established protocol using windod alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error in \\(\\log D_{cw}\\) of almost 4 log units and an overall signed error of \u22123 compared to experimental data. There was no substantial overall difference in accuracy beten simulating in NVT and NPT ensembles. The signed error suggests a systematic error but the experimental \\(D_{cw}\\) data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations."}]