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Do we need to do Equilibriation step even for the MD simulation of 100ps?
- sagar
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3 years 10 months ago #8583
by sagar
Do we need to do Equilibriation step even for the MD simulation of 100ps? was created 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
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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- vainikka
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3 years 10 months ago #8585
by vainikka
Replied by vainikka on topic Do we need to do Equilibriation step even for the MD simulation of 100ps?
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.
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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3 years 10 months ago #8586
by sagar
Replied by sagar on topic Do we need to do Equilibriation step even for the MD simulation of 100ps?
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?
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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3 years 10 months ago #8587
by vainikka
Replied by vainikka on topic Do we need to do Equilibriation step even for the MD simulation of 100ps?
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.
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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