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

From: Peter Košovan
Subject: Re: [ESPResSo-users] AdResS - state of the art
Date: Thu, 21 Nov 2013 18:06:17 +0100

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.



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.


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

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
Tel. +420221951290
Fax +420224919752

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