QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: job314 on May 13, 2020, 04:30
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Dear all, what would be a quick way using Windows version of QuantumATK Q-2019.12-SP1 to construct a box, fill it it water molecules and run some MD simulation to obtain a low energy structure for DFT optimization? The building of bulk water by hand is tedious and naturally it's not correct bonding anyways
thank you
Jonas
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Have you tried to use Packmol in builder? Using the Packmol, you can quickly fill water molecules in a box.
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In addition to using Packmol to construct the box with randomly positioned H2O molecules, a simple Force-Field based geometry optimization (minimization of both forces on atoms and stress on the supercell) might give a good starting point for DFT.
Flow:
1. use Packmol to construct the box with randomly positioned H2O molecules (perhaps aim for experimental density of molecules).
2. change cell type from UnitCell to SimpleCubic.
3. use ForceField calculator and OptimizeGeometry to relax forces and stress (take care to select a force field that actually works for water).
Example script attached. Runs in 2 mins on a laptop. Resulting water structure looks pretty OK to me, especially with the expected directional non-covalent bonding between H and O on different molecules.
If you believe finite-temperate molecular dynamics is needed to get better or more realistic water structure, that is also an option, but less simple than flow given above.