[gmx-users] Implicit solvent & PBC

Xavier Periole X.Periole at rug.nl
Fri Sep 19 17:39:22 CEST 2008 

On Fri, 19 Sep 2008 17:25:41 +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 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
Thanks for the ref. was not aware of it.
> 
>> > 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.
I agree with you. PBC have solved the boundary (spherical, walls, etc)
artifacts that were problematic in the early days of MD simulations.
No question about this.
My point was that the protein is not supposed to see its images so its
alone in an infinite solution.
PME introduces periodicity ... I do not like the idea but on the other hand
you are right that it solves other problems and as you say the use of
a large system basically removes the artifacts ...
Note that large cutoffs would do a good job for the 1/r, but no FF has been
parameterized for this!
> 
> 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
>> >> -----------------------------------------------------
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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
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