QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: hadhemat on April 21, 2022, 16:25
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Dear all,
I am doing classical MD simulations for a system including 1000 peptide molecules above a surface. I want to model the absorption of the molecules from the solvent on this surface. I was thinking how I can include the influence of gravity in this process. I was thinking in reality the gravity also will push the molecules down towards the surface. If I somehow could include an external force on (all) molecules (or atoms) in a specific direction, I can include gravity effect. I went through the manual and I think it is possible to do it by hook function but I can not make the script. Would you please help me make the script for such purpose? or possibly give me the script? Thank you
Best regards,
Hadi
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Any help please???
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I believe you can neglect a gravity effect, given it is much smaller compared, e.g., with dispersion (van der Waals) interaction, unless this simulation is meant to describe this process on a surface of a neutron star.
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Though gravity can be neglected, still how to use hook function in MD simulations?
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It will not affect any results as it will just result in a constant drift of all atoms. Unless of course some atoms are suspended and don't "fall", but even so we are talking about an effect maybe 10^30 times smaller than anything else so why bother - we don't have enough decimals the floating point representation of the computer to even add such numbers together...
Anyway, here is an example of how to use hook functions: https://docs.quantumatk.com/manual/Types/StrainConfigurationHook/StrainConfigurationHook.html