normal Do we need to do Equilibriation step even for the MD simulation of 100ps?

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2 months 4 days ago #8583 by sagar
Hello sir,
I am performing a short simulation for 100 ps. Do I need to perform equilibration steps for this short simulation also? help me with this

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2 months 4 days ago #8585 by vainikka
Hi,

Yes, you will need to equilibrate your system.

I can't really imagine why you would like to use Martini for a 100 ps simulation, or what type of useful data you would get from such a simulation.

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2 months 3 days ago #8586 by sagar
Thank you for reply, Vainikka

I am just testing that the mdp file i have created its working or not. later on I am going to perform 12 us simulation.

I want to ask you one more question that

I have .mdp file for a final production run, if I want to make .mdp file for equilibration, what changes I need to do in that? Do i need to decrease step size only?

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2 months 3 days ago #8587 by vainikka
Hi,

I think most people have their own way of equilibrating their systems, since there's really no strict protocol to follow. Depending on your system size and how easily it gives you trouble, you can either run something like a 500 ns equilibration with the same conditions as you would run your production run, or split the equilibration procedure in to multiple sections, where you start with a lower time step, and gradually increase it to the time step you were hoping to use in the production run.

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