On Apr 18, 2012, at 8:24 PM, "Andrew DeYoung" <[email protected]> wrote:
> Hi, > > Thank you, Justin, for your time! > > By reading the post that you sent > (http://lists.gromacs.org/pipermail/gmx-users/2004-March/009650.html), it > seems that epsilon_r is just a scale factor. I interpret this as meaning > that if, for example, I use epsilon_r = 2, then Coulomb interactions will be > scaled down by a factor of 2. That is, the Coulomb potential > (1/(4*pi*epsilon0))*(q_i q_j)/|r_i - r_j| will be multiplied by 1/2. > > But even if my interpretation is correct, what does this mean? epsilon_r > does not seem to be a reaction field parameter, since the value of epsilon_r > affects the electric potential that I calculate even though I am not using > implicit solvent, nor am I using one of the reaction field electrostatics > methods. Or, a different way to phrase this is, if most or all modern force > fields are parametrized based on epsilon_r and if one is not using any sort > of implicit or coarse-grained solvent or applying a reaction field > electrostatics method, then why would anyone want to scale down the Coulomb > potential? > 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. > Also, I am wondering about the boundary condition for the Ewald method. It > seems that, for the Ewald method, one must specify the dielectric constant > at the boundary. For example, the text on liquid simulations by Allen and > Tildesley says (page 157), "... we must specify the nature of the medium > surrounding the sphere, in particular its relative permittivity (dielectric > constant). The results for a sphere surrounded by a good conductor such as > a metal (epsilon = infinity) and for a sphere surrounded by vacuum (epsilon > = 1) are different [de Leeuw, Perram, and Smith 1980]." > > My question is, what epsilon parameter in Gromacs serves this purpose. One > possibility is epsilon_surface. However, this does not seem to be the right > parameter, because the manual entry for epsilon_surface says, "Turn it on by > setting it to the value of the relative permittivity of the imaginary > surface around your infinite system." This wording almost seems to imply > that it is a dipole correction (not a dielectric boundary condition), and > that there is some other parameter that, in fact, controls the "relative > permittivity of the imaginary surface." Is this true? If so, what is this > parameter? > > Thank you for your time! > > Andrew DeYoung > Carnegie Mellon University > > Andrew DeYoung wrote: >> Hi, >> >> What is the parameter epsilon_r mentioned in the manual >> (http://manual.gromacs.org/current/online/mdp_opt.html#el)? The manual > says >> that it is the relative dielectric constant. My initial thought was that >> this would only be relevant for reaction-field electrostatics, or > somewhere >> where implicit solvent is used. However, it seems that epsilon_rf (not >> epsilon_r) is used for reaction-field purpose. >> >> I am not using implicit solvent in my system, nor am I using a >> reaction-field method (I am using PME electrostatics); in my system, I am >> using an all-atom description. Then, does epsilon_r generate "additional" >> dielectric, beyond what naturally arises from the all-atom description of >> the solvent? >> >> Even though I am not using a reaction-field method, epsilon_r is clearly >> affecting something, because when I use g_potential to calculate the >> electric potential, the results vary considerably depending on the value > of >> epsilon_r that I use in my .mdp file. >> >> Do you have any thoughts about what epsilon_r does in an all-atom > descripton >> of a solvent? Does it provide "additional" charge screening? >> > > http://lists.gromacs.org/pipermail/gmx-users/2004-March/009650.html > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
