[gmx-users] Poisson equation, Hydrodynamic interaction

[David van der Spoel]

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