[gmx-developers] PME-Switch vs. PME
hess at kth.se
Thu Mar 7 11:05:04 CET 2013
I am sorry to hear about your unfortunate run setup.
I will put a note on the deprecation and a warning for large switching
range in 4.6.2.
On 03/07/2013 10:41 AM, Michel Cuendet wrote:
> Dear Berk,
> Thanks for your immediate reply. And I apologize for not providing the
> relevant cutoffs. Indeed I had a long switching range.
> OK Whow. So it is exactly as I feared, all my simulations are flawed.
> Being a big proponent of energy conservation, when 4.5 came out, I
> thought PME-switch was like the new state-of-the-art scheme (without
> properly checking what it was doing, my bad...). Now I realize that it
> is not. It is even quite wrong, as it probably introduces a sign
> reversal in the force around rcoulomb. As you mentioned, switching can
> be attained in a safe and consistent way using ewald_rtol.
> It seems to me that the PME-switch option is very dangerous. As you
> suggest I think it should be deprecated or at least it should be
> accompanied with a serious warning.
> Thanks for your help,
> On Mar 6, 2013, at 7:34 PM, gmx-developers-request at gromacs.org
> <mailto:gmx-developers-request at gromacs.org> wrote:
>> Message: 4
>> Date: Wed, 06 Mar 2013 19:29:19 +0100
>> From: Berk Hess <hess at kth.se <mailto:hess at kth.se>>
>> Subject: Re: [gmx-developers] PME-Switch vs. PME
>> To: Discussion list for GROMACS development
>> <gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>>
>> Message-ID: <51378AFF.9020201 at kth.se <mailto:51378AFF.9020201 at kth.se>>
>> Content-Type: text/plain; charset="iso-8859-1"
>> You don't mention your, critical, cut-off parameters.
>> I guess you used a long switching range. The switch is only intended to
>> cut-off artifacts (and therefore does not act on the reciprocal).
>> Any switching function should only be applied over a very short range.
>> As with PME ewald_rtol is usually 10^-5, you don't really need the
>> and if you do want to use it, you should switch over 0.05 nm or less.
>> But in 4.6 you can use exact cut-off's, either with the Verlet cut-off
>> or at a high cost also with the group cut-off scheme. Thus PME-switch is
>> no longer needed
>> and we should deprecate it in 4.6.
> Michel Cuendet, PhD
> Molecular Modeling Group
> Swiss Institute of Bioinformatics
> CH-1015 Lausanne
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