[gmx-users] Poisson equation, Hydrodynamic interaction

[Amin Rouy]

Thank you very much dear Alex and David. I got my answers.

On Sun, Mar 25, 2018 at 12:40 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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>
>> 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
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
>
> --
> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>