On Fri, 19 Sep 2008 16:49:45 +0200
Berk Hess <[EMAIL PROTECTED]> wrote:
From: [EMAIL PROTECTED]
Subject: Re: [gmx-users] Implicit solvent & PBC
To: [email protected]
Date: Fri, 19 Sep 2008 16:42:15 +0200
On Fri, 19 Sep 2008 15:00:18 +0200
Berk Hess <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED]
>> Subject: Re: [gmx-users] Implicit solvent & PBC
>> To: [email protected]
>> Date: Fri, 19 Sep 2008 14:52:39 +0200
>>
>> On Fri, 19 Sep 2008 17:28:20 +0530 (IST)
>> Anirban Ghosh <[EMAIL PROTECTED]> 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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>
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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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