Re: [ESPResSo-users] AdResS - state of the art

[Peter Košovan]

Just to add to what Olaf said: if you want to simulate atomistic, you should to carefully think of the value of the Bjerrum length as a parameter for electrostatics. Some weeks ago we had a discussion on this mailing list about the meaning of Bjerrum length when the solvent is not a continuum.

Regards,

peter

2013/11/21 Olaf Lenz <address@hidden>

Technically, it is of course possible. However, ESPResso does not have built in force fields, so setting them up is pretty tedious. Furthermore, ESPResSo might get into trouble when you need to define too many different types of particles and their interactions. All-atom simulations usually have a great deal more particle types than our top-down particle types, so this might cause a problem.

Olaf

2013/11/21 Jakub Krajniak <address@hidden>

On Thu, Nov 14, 2013 at 4:17 PM, Christoph Junghans <address@hidden> wrote:
>
> Hi Jakub,
>
(...)

>
> To get a fair answer, you should also ask the same question on
> espresso-pp mailing list!
>
> When Simon and I wrote the AdResS code for ESPResSo, we had to fit it
> into an existing MD package, while ESPResSo++  was designed with
> having AdResS in mind. So, like Olaf said,  ESPResSo has a
> proof-of-concept implementation, which is an extension to normal MD
> while in ESPResSo++ AdResS is part of the MD core.
>
> The AdResS code in ESPResSo hasn't been used very extensively in
> recent years due to the fact that the center of AdResS development,
> MPI-P, is also developing ESPResSo++. And because AdResS is also part
> of Gromacs 4.6, which will be most likely your best choice, if you
> want to use AdResS to speed-up simulations. An estimate for the
> speedup in ESPResSo/Gromacs can be found on the slides of my 2012 talk
> at the ESPResSo cecam tutorial.
>

Thanks for making the situation much more clear what tools to use as a foundation!

I rather want to experiment with the AdResS for some other setup so Espresso is

more flexible than Gromacs. 

One more question, related to the Espresso itself. I saw somewhere the comment that 

Espresso is not design to run the all-atom md simulation. In what sense is that? Cause

as I briefly go through the documentation, it seems that technically it is possible to create

all-atom setup with defined desired interaction and run it.

Best regards,
Jakub Krajniak

-- 

PhD student at the department of computer science

KU Leuven

--

Dr. rer. nat. Olaf Lenz

Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart

Phone: +49-711-685-63607

--

Dr. Peter Košovan

Departmtent of Physical and Macromolecular Chemistry

Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie

Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951290

Fax +420224919752