Dear All,
We wanted to build computational models of hydrophobic and hydrophilic self-assembled monolayers (SAMs) for MD Simulation experiments. There are a few papers where the simulation structure of self-assembled monolayers was generated by creating a fixed 2D grid of sulphur atoms in a diamond geometry (PNAS, 113(16), 4332-4337). However, I could not find a detailed explanation of how the initial model was constructed. There were a few pertinent questions in my mind such as-
(i) How many numbers of sulphur atoms were taken in a grid?
(ii) How were the sulphur atoms connected in diamond geometry?
(iii) How were the SAM chains held to each other during the simulation?
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