[gmx-developers] jenkins LJ-PME verify failures expected

[Berk Hess]

On 01/24/2014 09:03 AM, David van der Spoel wrote:
> On 2014-01-22 21:24, Mark Abraham wrote:
>> Not serious, unless you ran them on the GROMACS beta!
>> (https://gerrit.gromacs.org/#/c/3018/)
>
> Is that irony?
>
> This in principle means the long range exclusion corrections for LJPME 
> were wrong, or not? And hence no energy conservation, and all results 
> in Christian's paper are wrong and also the runs we have done?
Strictly speaking yes.

The forces on directly constrained atoms are irrelevant, since those are 
removed anyhow.
The forces on 1-3 and 1-4 do matter.
I ran a quick test of a protein in Amber with cut-off 1 nm and default 
PME settings. I get fscal values between -2 and -1.  Part of this will 
be canceled by constraints. I don't think such small force errors will 
affect the results measurably, also because there is little flexibility 
in 1-3 and 1-4 distances.
Note that the energies are correct.

Cheers,

Berk
>
>
>
>
>>
>> Mark
>>
>>
>> On Wed, Jan 22, 2014 at 6:18 PM, David van der Spoel
>> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>>
>>     On 2014-01-22 18:04, Mark Abraham wrote:
>>
>>         Hi,
>>
>>         We fixed a bug today in LJ-PME, which has been fixed and merged,
>>         along
>>         with matching changes to the regressiontest suite. So you should
>>         expect
>>         that code based on earlier versions will now fail to verify with
>>         Jenkins
>>         on the three complex/ljpme* tests. Please rebase as/when it
>>         suits you -
>>         but remember that reviewers will prefer you to separate a change
>>         of base
>>         and a change of content into two actions on Gerrit!
>>
>>         Thanks,
>>
>>         Mark
>>
>>
>>     something serious? We're about to submit a paper with 500 LJPME
>>     simulations.
>>
>>     --
>>     David van der Spoel, Ph.D., Professor of Biology
>>     Dept. of Cell & Molec. Biol., Uppsala University.
>>     Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
>>     <tel:%2B46184714205>.
>>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>>     http://folding.bmc.uu.se
>>     --
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