unanswered Relative dielectric constant

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1 month 1 week ago #7921 by sk
sk created the topic: Relative dielectric constant
Hi,

I have a system which consists, in part, 2 alpha-helices with charged side-chains. I'm trying to compute the free energy as a function of the distance between these 2 alpha-helices using metadynamics.

In all-atom simulations, the free energy profile is as expected; high when they are close together (due to the electrostatic repulsion among other things) and it falls off gradually as they move further apart.

However, this effect is completely lost when I attempt to do the simulation with a CG version of the system. This is probably because of the high relative dielectric constant used with martini. If I drop epsilon_r from 15 to about 7, it somewhat reproduces the free-energy profile obtained from all-atom simulation.

I'm worried that changing the relative dielectric constant might have some other adverse effect. How should I go about verifying whether it does or doesn't for my system?

(Note: I've also tried it with polarizable water, it didn't improve the results much. So I've just stuck with non-polarizable water for faster simulation times)

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