normal NPT vs. NPT ensemble for equilibration in AA compared to coarse-grained?

  • Anna Stephens
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1 year 8 months ago #9520 by Anna Stephens
Hey,

In atomistic simulations we tend to begin equilibration with the NVT ensemble to get the temperature correct, followed by the NPt ensemble to stabilize density and pressure? When I've used MARTINI MAKER on CHARMGUI, all the equilibration files do not change so much other than it being semi-isotropic pressure coupling for the system (which remains that way) and the timestep and number of steps change.

I suppose my question is how come there is a difference for coarse-grained martini in comparison to full atomistic?

Thanks so much!

Anna

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1 year 6 months ago #9555 by riccardo
I'm not familiar with what they do in the Martini Maker of Charmm-GUI but NVT/NPT protocols used in AA are similar to the ones used in Martini simulations. The only difference perhaps is that usually an NVT eq. step is not required and you can jump directly to an NPT step and equilibrate T and density at once. Be sure to use the parameters as recommended at cgmartini.nl/index.php/force-field-parameters/input-parameters (top of the page). semi-isotropic coupling makes sense for a lipid membrane (or similar system) but not always. Again, use the same considerations that apply to AA systems. Hope this helps

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