[gmx-users] Poisson equation, Hydrodynamic interaction
David van der Spoel
spoel at xray.bmc.uu.se
Sun Mar 25 12:40:04 CEST 2018
Den 2018-03-24 kl. 23:45, skrev Amin Rouy:
> Dear Mark, I have already checked the manual then wrote the question here.
> Dear Alex, what I mean is simply when we have a metal surface in contact
> with charged fluid, boundary condition at surface E=0 leads to different
> result of Poisson equation (image charges method). So does Gromacs do that?
> Dear David, it is a fluid dynamic concept. When an object moves inside a
> fluid, it feels some force (hydrodynamic force), and if more than one body
> moving in the fluid they feel some interactions due to each others
> movement. So does Gromacs gives hydrodynamic properties on immersed objects
> in a fluid?
It is a concept, that may be a good word. Now that we have direct
simulations we do not need these kind of concepts anymore. In the
simulation you can "measure" most physical observables, so why would you
try to extract non-physical observables such as "hydrodynamic
interactions"? If you wish you can compare the simulation results to
analytical theories but since both MD simulations and analytical
theories are inexact such a comparison may or may not be meaningful.
> On Sat, Mar 24, 2018 at 9:48 PM, David van der Spoel <spoel at xray.bmc.uu.se>
>> Den 2018-03-24 kl. 20:29, skrev Amin Rouy:
>>> I have 2 questions please?
>>> 1- Is Gromacs able to simulate metallic system (Poisson equation should be
>>> solved at the surface)
>>> 2- is Gromacs able to calculate hydrodynamic interactions?
>> What are hydrodynamic interactions? This is a serious question.
>> My anwsers would be
>> 2a) there is no such thing as a hydrodynamic "interaction"
>> 2b) yes, gromacs can calculate transport properties such as diffusion
>> (equilibrium MD simulations) and viscosity (equilibrium and non-equilibrium
>> MD) and effective interactions between particles (through
>> potential-of-mean-force calculations). All of these are well established
>> techniques. The accuracy of the results depends as always on the force
>> field and the sampling.
>>> On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy <aminrou1986 at gmail.com> wrote:
>>>> I have 2 questions please?
>>>> 1- Does Gromacs ability to solve Poisson equation, e.g. boundary
>>>> on metal surface?
>>>> 2- is Gromacs able to calculate hydrodynamic interactions?
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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