Thing I want to do –
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Simulated Annealing of a Polymer
Methodology I am following –
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Create a Polymer chain of desired length.
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Use PACKMOL to pack desired number of chains in a conveniently huge box.
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Using LAMMPS follow the general equilibration protocol, NVE, NVT, NPT dynamics.
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Shrink the box size using NPT dynamics to get desired density. Output density using ‘thermo_style custom’ command.
Issues –
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When I shrink the box size with ‘fix npt’ with Pstart and Pstop values as 1 1 and run the simulation for enough period of time, I am nowhere close to my desired density.
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To overcome this I increase the pressure being applied on the system. With trial and error, I figure out that using 1GPa of pressure on the system brings me closer to desired density of the system.
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Everything’s good. Pstart and Pstop are 1GPa and the density outputted at the end of the run is close to the expected density of the system.
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Now when I try to equilibrate the system, the system volume increase and density drops down rapidly. Now I realise that is because the pressure on the system has been released.
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A NPT at 1GPa followed by the NVT with no barostatting, it is obvious that system pressure will drop down and eventually lead to decrease in the density.
Problem –
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I want to perform Simulated Annealing at atmospheric pressure and not 1GPa. How do I maintain the density of the system even after the pressures is released ?
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Am I following the right protocol ? Or does it make no sense ?
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Also, please point me towards understanding forcefields.
Edit – Providing more data, Polymer – Polyethylene. Force field – Dreiding Potential. Not a liquid system, just the polymer.
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