[gmx-users] Implicit solvent & PBC

[Xavier Periole]

On Fri, 19 Sep 2008 16:49:45 +0200
  Berk Hess <gmx3 at hotmail.com> wrote:
> 
> 
> 
> 
>> From: X.Periole at rug.nl
>> Subject: Re: [gmx-users] Implicit solvent & PBC
>> To: gmx-users at gromacs.org
>> Date: Fri, 19 Sep 2008 16:42:15 +0200
>> 
>> On Fri, 19 Sep 2008 15:00:18 +0200
>>   Berk Hess <gmx3 at hotmail.com> wrote:
>> > Hi,
>> > 
>> > The same as in normal simulations.
>> > I always use PME and PBC in my implicit solvent simulations.
>> then -
>> PME: treament of long range electrostatic interactions in implicit solvent?
>> PBC: simulate infinite dilution again in implicit solvent?
>> 
>> I really do not see the point!
> 
> I have for instance systems with ions in implicit solvent.
> Since ions have long range electrostatic interactions, you need 
> PME (and PBC).
Then of course. I actually thought that might be your case. Is it
actually worth? Are they behaving reasonably, not sticking to anything
they meet? How did you parameterize these funny ones?
> Because it is implicit solvent you need to use the appropriate epsilon_r.
> 
> I don't see what PBC has to do with infinite dilution.
That is the original idea of using PBC: simulate a molecule in a box of
solvent that would not have boundaries=infinite dilution. The concept has
derived towards "periodic systems" but it is not supposed to be. This is
why I generally do not use PME.
> 
> Berk
> 
>> Tsjerk might have a point with crystal packing ...
>> > 
>> > Berk
>> > 
>> > 
>> >> From: X.Periole at rug.nl
>> >> Subject: Re: [gmx-users] Implicit solvent & PBC
>> >> To: gmx-users at gromacs.org
>> >> Date: Fri, 19 Sep 2008 14:52:39 +0200
>> >> 
>> >> On Fri, 19 Sep 2008 17:28:20 +0530 (IST)
>> >>   Anirban Ghosh <anirbanz83 at yahoo.co.in> wrote:
>> >> > Hi All,
>> >> > 
>> >> > I am simulating a Coarse Grained model using implicit solvent 
>>condition. 
>> >>Can 
>> >> >Periodic Boundary Condition and Particle-Mesh-Ewald be used with 
>>implicit 
>> >> >solvent simulation? 
>> >> What would be the use of PME and PBC in implicit solvent?
>> >> > Thanks,
>> >> > 
>> >> > 
>> >> > 
>> >> > 
>> >> > Anirban Ghosh
>> >> > M.Tech Bioinformatics
>> >> > University of Hyderabad
>> >> > 
>> >> > 
>> >> > 
>> >> >      Unlimited freedom, unlimited storage. Get it now, on 
>> >> >http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
>> >> 
>> >> -----------------------------------------------------
>> >> XAvier Periole - PhD
>> >> 
>> >> Molecular Dynamics Group / NMR and Computation
>> >> University of Groningen
>> >> The Netherlands
>> >> -----------------------------------------------------
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>> -----------------------------------------------------
>> XAvier Periole - PhD
>> 
>> Molecular Dynamics Group / NMR and Computation
>> University of Groningen
>> The Netherlands
>> -----------------------------------------------------
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-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------