[gmx-users] Re: What is epsilon_r?

[David van der Spoel]

On Apr 18, 2012, at 9:10 PM, "Andrew DeYoung" <adeyoung at andrew.cmu.edu> wrote:

> Dr. van der Spoel,
> 
> Thank you for your time!  So it seems that epsilon_r is just a "fudge
> factor" and has nothing to do with the dielectric constant at the boundary
> of the "PME/Ewald sphere."  Is that dielectric constant actually
> epsilon_surface?  I am not very familiar at all with other MD codes, but a
> colleague recently told me that some other codes use a default dielectric
> constant of infinity at the surface.  However, in Gromacs, the default value
> of epsilon_surface is 0, which corresponds (I guess) to "no dielectric" at
> the surface.  Is this true?
No, zero means in fact infinity and this is the default. Only for very special cases should you change this.
> 
> Also, to complicate things further, I am using a pseudo 2-D PME summation
> (ewald_geometry = 3dc).  I have read in the manual entry for epsilon_surface
> that epsilon_surface "does not affect the slab 3DC variant of the long range
> corrections."  If you have time, what does this mean?  Does this mean that,
> if I use ewald_geometry = 3dc, then there is "no dielectric" at the surface
> (the medium surrounding the "Ewald sphere")?

The 3dc only affects the dipole correction if I remember correctly. If you use it a refernce to a paper appears in your log file.
> 
> Thank you!
> 
> Andrew DeYoung
> Carnegie Mellon University
> 
>> epsilon_r should never be used with a regular force field because the
>> balance between coulomb and other terms will be wrong. maybe we should
>> remove the term. 
> 
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