[gmx-developers] PME-Switch vs. PME

[Berk Hess]

Hi,

I field an issue: http://redmine.gromacs.org/issues/1179
and uploaded a fix: https://gerrit.gromacs.org/#/c/2220/

Cheers,

Berk

On 03/07/2013 11:05 AM, Berk Hess wrote:
> Hi,
>
> 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.
>
> Cheers,
>
> Berk
>
> 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,
>> Michel
>>
>>
>> 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"
>>>
>>> Hi,
>>>
>>> You don't mention your, critical, cut-off parameters.
>>> I guess you used a long switching range. The switch is only intended to
>>> avoid
>>> 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 
>>> switch,
>>> 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
>>> scheme,
>>> 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.
>>>
>>> Cheers,
>>>
>>> Berk
>>
>> ==========================================================
>> Michel Cuendet, PhD
>> Molecular Modeling Group
>> Swiss Institute of Bioinformatics
>> CH-1015 Lausanne
>> Switzerland
>> http://lausanne.isb-sib.ch/~mcuendet/ 
>> <http://lausanne.isb-sib.ch/%7Emcuendet/>
>> ==========================================================
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
>

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