[gmx-users] Implicit solvent & PBC

Fri Sep 19 17:25:41 CEST 2008

> From: X.Periole at rug.nl
> Subject: Re: [gmx-users] Implicit solvent & PBC
> To: gmx-users at gromacs.org
> Date: Fri, 19 Sep 2008 17:03:08 +0200
> 
> 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?

If you do everything systematically and correct it does (nearly) exactly what
an all-atom simulation does, see:

   B. Hess, C. Holm and N. van der Vegt 

  Modeling Multibody Effects in Ionic Solutions with a Concentration Dependent Dielectric Permittivity  

   Phys. Rev. Lett. 96, 147801 (2006)
http://dx.doi.org/10.1103/PhysRevLett.96.147801

> > 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.

I don't agree with this.
PBC is very useful for crystals.
For non-periodic systems PBC is still the best solution,
since using any boundary produces more artifacts.

Electrostatic interactions go as 1/r.
A full electrostatics solver, such as PME, is the only way to get the full 1/r.
Any other methods does not produce the correct 1/r interaction.
If PME produces artefacts, your unit-cell is too small.
This is not a problem of PME, but of your system size.

Berk

> > 
> > 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
> >> -----------------------------------------------------
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at gromacs.org
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> -----------------------------------------------------
> XAvier Periole - PhD
> 
> Molecular Dynamics Group / NMR and Computation
> University of Groningen
> The Netherlands
> -----------------------------------------------------
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