[gmx-users] Implicit solvent & PBC

[Berk Hess]

> 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).
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.

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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