Author Topic: Including the gravity effect in MD simulations!  (Read 319 times)

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Offline hadhemat

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Including the gravity effect in MD simulations!
« on: April 21, 2022, 16:25 »

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

Offline hadhemat

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Re: Including the gravity effect in MD simulations!
« Reply #1 on: April 23, 2022, 13:36 »
Any help please???

Offline Petr Khomyakov

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Re: Including the gravity effect in MD simulations!
« Reply #2 on: May 5, 2022, 14:24 »
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. 

Offline AsifShah

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Re: Including the gravity effect in MD simulations!
« Reply #3 on: May 8, 2022, 09:20 »
Though gravity can be neglected, still how to use hook function in MD simulations?

Offline Anders Blom

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Re: Including the gravity effect in MD simulations!
« Reply #4 on: June 2, 2022, 02:01 »
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