[gmx-users] Poisson equation, Hydrodynamic interaction

Alex nedomacho at gmail.com
Sun Mar 25 04:47:49 CEST 2018

```I answered your question earlier: Gromacs forcefields do not do that, so
you cannot have a reasonable model of a metal surface. Further, E = 0
only holds for a perfectly flat metal surface in the macroscopic sense
and the actual picture is a bit more intricate.
Your second question probably has to do with basic forces arising from
solid-fluid interactions (i.e. drag) and of course they would come out
of any reasonable forcefield.

Alex

On 3/24/2018 4:45 PM, Amin Rouy wrote:
> 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?
>
>
>
> On Sat, Mar 24, 2018 at 9:48 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>
>> Den 2018-03-24 kl. 20:29, skrev Amin Rouy:
>>
>>> Hi,
>>>
>>> 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.
>>
>>
>>
>>> thanks.
>>>
>>>
>>> On Fri, Mar 23, 2018 at 1:04 PM, Amin Rouy <aminrou1986 at gmail.com> wrote:
>>>
>>> Hi,
>>>> I have 2 questions please?
>>>>
>>>> 1- Does Gromacs ability to solve Poisson equation, e.g. boundary
>>>> condition
>>>> on metal surface?
>>>>
>>>> 2- is Gromacs able to calculate hydrodynamic interactions?
>>>>
>>>> thanks
>>>>
>>>>
>> --
>> 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.
>> http://www.icm.uu.se
>>
>> --
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```