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Extending Non-Equilibrium Pulling Method in GROMACS with Arbitrary User-Defined Atom Weight Factor Expressions - GASERI
Third Infinity 2022
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Extending Non-Equilibrium Pulling Method in GROMACS with Arbitrary User-Defined Atom Weight Factor Expressions - Vedran Miletić , Matea Turalija - 😎 Group for Applications and Services on Exascale Research Infrastructure, Faculty of Informatics and Digital Technologies, University of Rijeka - Third Infinity 2022 , Max Planck Institute for Multidisciplinary Sciences , Göttingen, 23rd of September 2022 - Outline - Molecular dynamics simulation - Non-equilibrium pulling - Pull coordinate - Pull groups and force - Processes activated by flow - Simulating uniform flow (1/3) - Simulating uniform flow (2/3) - Simulating uniform flow (3/3) - The previous approach (1/4) - The previous approach (2/4) - The previous approach (3/4) - Each atom is weighted with the weight factor: Coordinate \(x\) of each atom in the arbitrary slice is normalized from the interval \([s_{min}, s_{max}]\) to the coordinate \(x_{unit}\) in the interval \([−1, 1]\) : The previous approach (4/4) - The new, general approach (1/3) - The new, general approach (2/3) - The new, general approach (3/3) - Possible applications of atom weight factor expressions - Future plans - Acknowledgments - How to play with the code - Questions? GROMACS developer workshop - Author: Vedran Miletić