2018
DOI: 10.5281/zenodo.1247565
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Bobbypaton/Goodvibes: Goodvibes V2.0.2

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Cited by 2 publications
(3 citation statements)
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“…Before geometry optimization via ab initio methods, initial configurations were picked via conformational analysis using MacroModel and an OPLS-based force field, where structures with dentation matching those from the classical MD simulations were picked. In order to correct for spurious contributions of low-frequency modes to the vibrational partition function, Truhlar’s correction was applied using Patton’s code …”
Section: Methodsmentioning
confidence: 99%
“…Before geometry optimization via ab initio methods, initial configurations were picked via conformational analysis using MacroModel and an OPLS-based force field, where structures with dentation matching those from the classical MD simulations were picked. In order to correct for spurious contributions of low-frequency modes to the vibrational partition function, Truhlar’s correction was applied using Patton’s code …”
Section: Methodsmentioning
confidence: 99%
“…21,22 We note that the translational contribution calculated from the Sackur-Tetrode equation 23 is here evaluated for the appropriate standard concentration (1 mol/L), and that vibrational frequencies below 100 cm −1 are adjusted to 100 cm −1 to avoid spurious entropy contributions. 13,24,25 Furthermore, all calculations to obtain S and E thermal were undertaken using the PCM with a single dielectric constant, that of 2-methoxyethanol ( = 16.96), as variations calculated for S and E thermal across various are negligible. A detailed example for the application of equation 4 is provided in the supplementary information (SI).…”
Section: Partial Explicit Solvation Shell-in Order To Calculate the F...mentioning
confidence: 99%
“…Corrections to the thermodynamic data were undertaken with the Good-Vibes analysis code. 25 Initial configurations were found via conformational analysis [29][30][31][32] and energy minimization using the MacroModel package 33 with the semi-empirical OPLS forcefield. 34 Full explicit solvation shell.-Electrostatic energies calculated with the above presented model are only accounted for by a single explicit solvent molecule and a structureless dielectric medium.…”
Section: Partial Explicit Solvation Shell-in Order To Calculate the F...mentioning
confidence: 99%